A place in the semi-final looked a formality as Chelsea struggled to make any impression - only for the second half to see a complete transformation in fortunes.
Phil McNultyChief football writer, BBC Sport
"Benitez has been on a starvation diet when it comes to getting credit from Chelsea's supporters since he arrived in succession to sacked Roberto Di Matteo. They must find it in their hearts to afford him some here"
Chelsea interim manager Rafael Benitez once again felt the full fury of his own supporters when he replaced Frank Lampard and Victor Moses with Eden Hazard and Jon Obi Mikel not long after the restart.
The taunts were silenced by Hazard's superb strike just before the hour and another fine finish from Ramires soon after as Chelsea were revived in the most dramatic fashion.
And, as an enthralling tie reached its conclusion, Chelsea looked far more likely to secure a place in the FA Cup semi-finals and it took a save with his feet from United keeper David de Gea from Juan Mata a minute from time to deprive Benitez's side of victory.
Rooney was restored to United's starting line-up after being dropped against Real Madrid with Van Persie moving down to the role of substitute - and it was almost inevitable he would have an impact on the early events that saw United take command.
United were ahead after five minutes with a goal that owed almost as much to its creator Michael Carrick as goalscorer Hernandez.
The England midfielder showed wonderful vision with a long, angled pass into the area that left Chelsea keeper Petr Cech in two minds, but it still required clever movement and a fine header from Hernandez to score.
It was exactly what Benitez did not want and things got worse for Chelsea seven minutes later as United doubled their lead when Rooney's floated free-kick evaded all the bodies inside the area and Cech to drift in at the far post.
As Chelsea suffered this nightmare opening phase, captain John Terry could only watch from the sidelines as Benitez once again chose to leave him on the bench.
Chelsea, understandably, were pushed on to the back foot by the speed of United's start and almost fell further behind only for Cech to block Rooney from 10 yards and then produce great athleticism to save David Luiz's header from the rebound as it looked bound for the top corner.
As the half progressed, Chelsea settled and enjoyed more possession but failed to make the most of promising positions with either poor delivery or wayward finishing.
Chelsea made no impression on United early in the second half, prompting Benitez to remove Lampard and Moses for Hazard and Mikel.
Robbie SavageBBC Radio 5 live
"Chelsea looked vulnerable at the back in the first half but the problem was in their midfield, not in their defence. That changed in the second half. For starters Chelsea were a lot more compact in the middle of the pitch and they did not allow United the same amount of space.
"Eden Hazard was the key to their comeback, though. His pace and penetration meant he contributed more on his own than Chelsea's three attacking midfielders had managed between them before he came on."
The changes were greeted with jeers from Chelsea's supporters as they chanted "You don't know what you're doing" and "We want our Chelsea back" in the direction of Benitez.
And yet it was Hazard who brought Chelsea back into the game with a wonderful goal on the hour, using Rafael as a shield before curling a finish beyond United keeper De Gea.
The shift in momentum was enough to prompt Ferguson to replace Hernandez with Van Persie but Chelsea were really back in business after 67 minutes as they completed the turnaround.
Chelsea found space as they broke on United and when Oscar found Ramires, his Brazilian compatriot showed great composure to turn inside and send a precise left-foot finish into De Gea's bottom corner.
The emphasis had shifted completely with Chelsea looking the more likely winners and it was only a vital touch from De Gea's right-foot that stopped Mata giving Benitez's side the victory.
The Spaniard then saved again from Hazard as United end looking ragged and hanging on.
90:00+4:45 The referee blows his whistle to end the game.
90:00+4:07 Emboaba Oscar takes a inswinging corner from the left by-line to the near post.
90:00+3:45 Shot from 20 yards from Eden Hazard. Save by David De Gea.
90:00+3:08 Fernando Torres takes a shot. Save by David De Gea.
90:00+2:09 Free kick awarded for an unfair challenge on Michael Carrick by Juan Mata. Rio Ferdinand takes the direct free kick.
90:00+0:04 Inswinging corner taken right-footed by Eden Hazard from the left by-line, Jonny Evans makes a clearance.
89:38 Juan Mata takes a shot. David De Gea makes a save.
87:20 Antonio Valencia delivers the ball.
86:16 Corner taken by Juan Mata, Antonio Valencia makes a clearance.
86:01 Fernando Torres takes a shot. Blocked by Jonny Evans.
83:37 Shot by Juan Mata. David De Gea makes a save.
81:49 Foul by Robin van Persie on Gary Cahill, free kick awarded. Free kick taken by David Luiz.
79:19 Free kick awarded for a foul by Robin van Persie on David Luiz. Free kick taken by Petr Cech.
78:45 Robin van Persie has a drilled shot. Blocked by Cesar Azpilicueta.
76:44 Substitution Fernando Torres on for Demba Ba.
76:24 Shot by Tom Cleverley from just outside the area goes over the net.
76:10 Corner taken right-footed by Wayne Rooney from the left by-line, clearance by Gary Cahill.
74:54 Wayne Rooney delivers the ball from the free kick right-footed from left channel, clearance made by David Luiz. Robin van
Persie takes a shot. Blocked by Gary Cahill.
74:54 Substitution Danny Welbeck on for Shinji Kagawa.
74:54 Booking Booking for Eden Hazard for unsporting behaviour.
74:46 Tom Cleverley fouled by Eden Hazard, the ref awards a free kick.
74:14 Foul by Mikel on Tom Cleverley, free kick awarded. Direct free kick taken by Michael Carrick.
72:41 The ball is sent over by Shinji Kagawa, Gary Cahill makes a clearance.
71:48 Rafael Da Silva fouled by Eden Hazard, the ref awards a free kick. Rafael Da Silva takes the free kick.
70:34 The ball is crossed by Patrice Evra, Gary Cahill gets a block in.
70:13 Free kick awarded for a foul by David Luiz on Tom Cleverley. Direct free kick taken by Michael Carrick.
69:29 Free kick awarded for a foul by Tom Cleverley on Nascimento Ramires. Free kick taken by David Luiz.
67:21 The assist for the goal came from Emboaba Oscar.
67:21 GOAL - Nascimento Ramires:Man Utd 2 - 2 Chelsea Nascimento Ramires gets on the score sheet with a goal from the edge of the penalty box to the bottom left corner of the goal.
Man Utd 2-2 Chelsea.
66:59 Antonio Valencia delivers the ball, clearance by Cesar Azpilicueta.
61:42 Substitution (Man Utd) makes a substitution, with Robin van Persie coming on for Javier Hernandez.
61:18 The ball is crossed by Eden Hazard, David De Gea makes a comfortable save.
58:17 Juan Mata provided the assist for the goal.
58:17 GOAL - Eden Hazard:Man Utd 2 - 1 Chelsea A goal is scored by Eden Hazard from just inside the area to the top right corner of the goal. Man Utd 2-1 Chelsea.
57:40 David Luiz takes a shot. Save by David De Gea.
57:21 The ball is crossed by Cesar Azpilicueta.
54:30 Rafael Da Silva takes the direct free kick.
54:30 Booking David Luiz shown a yellow card.
54:23 David Luiz challenges Rafael Da Silva unfairly and gives away a free kick.
54:07 Eden Hazard sends in a cross, clearance made by Jonny Evans.
53:03 The ball is delivered by Rafael Da Silva, clearance by Cesar Azpilicueta.
51:29 Substitution Eden Hazard on for Victor Moses.
51:29 Substitution (Chelsea) makes a substitution, with Mikel coming on for Frank Lampard.
51:01 Nascimento Ramires has an effort at goal from just inside the box that misses to the left of the goal.
48:56 The ball is swung over by Antonio Valencia, David Luiz manages to make a clearance.
45:34 Juan Mata produces a cross, Rio Ferdinand makes a clearance.
45:01 The second half begins.
45:00+2:56 The referee blows for half time.
45:00+1:50 Wayne Rooney produces a right-footed shot from just outside the penalty area that goes harmlessly over the target.
45:00+1:27 Substitution Antonio Valencia replaces Luis Nani.
44:29 The ball is swung over by Javier Hernandez, Gary Cahill makes a clearance.
42:13 Tom Cleverley takes a shot. Gary Cahill gets a block in.
40:53 Patrice Evra restarts play with the free kick.
40:53 Booking Cesar Azpilicueta goes into the book for unsporting behaviour.
40:44 Cesar Azpilicueta concedes a free kick for a foul on Javier Hernandez.
40:03 The ball is swung over by Cesar Azpilicueta, save by David De Gea.
39:50 The ball is sent over by Ashley Cole.
38:30 Victor Moses has an effort at goal from deep inside the area missing to the left of the goal.
36:12 Free kick awarded for a foul by Nascimento Ramires on Shinji Kagawa. Free kick taken by Wayne Rooney.
35:43 The assistant referee signals for offside against Cesar Azpilicueta. David De Gea takes the free kick.
35:25 The ball is sent over by Victor Moses, Michael Carrick gets a block in.
31:27 Centre by Victor Moses, clearance by Rio Ferdinand.
31:12 The ball is sent over by Emboaba Oscar, blocked by Rafael Da Silva.
30:54 A cross is delivered by Emboaba Oscar, clearance made by Jonny Evans.
29:26 Demba Ba takes a shot. Save by David De Gea.
26:06 Shot from outside the box by Gary Cahill goes wide right of the target.
24:49 Inswinging corner taken from the left by-line by Wayne Rooney. Tom Cleverley takes a shot. Save by Petr Cech.
24:20 Wayne Rooney takes a shot. Save by Petr Cech.
23:22 Luis Nani sends in a cross, Javier Hernandez has an effort at goal from close range which goes wide right of the goal.
22:10 Demba Ba gives away a free kick for an unfair challenge on Tom Cleverley. David De Gea takes the direct free kick.
21:44 Frank Lampard takes a shot. Save by David De Gea.
21:17 Luis Nani delivers the ball, comfortable save by Petr Cech.
20:40 Cesar Azpilicueta delivers the ball, Michael Carrick manages to make a clearance.
19:11 Victor Moses takes a shot. Jonny Evans gets a block in.
18:48 Rafael Da Silva concedes a free kick for a foul on Ashley Cole. David Luiz takes the free kick.
18:10 Ashley Cole sends in a cross, Rio Ferdinand gets a block in.
14:35 Free kick awarded for a foul by Cesar Azpilicueta on Rio Ferdinand. David De Gea restarts play with the free kick.
13:39 Tom Cleverley is penalised for handball and concedes a free kick. The free kick is swung in left-footed by Juan Mata, clearance
by Rio Ferdinand.
12:28 Shinji Kagawa concedes a free kick for a foul on Nascimento Ramires. David Luiz takes the direct free kick.
10:15 Assist on the goal came from Luis Nani.
10:15 GOAL - Wayne Rooney:Man Utd 2 - 0 Chelsea Goal scored by Wayne Rooney from just outside the area to the top right corner of the goal. Man Utd 2-0 Chelsea.
9:38 Victor Moses concedes a free kick for a foul on Luis Nani. Wayne Rooney crosses the ball in from the free kick,
9:02 Inswinging corner taken from the left by-line by Emboaba Oscar, Jonny Evans manages to make a clearance.
8:47 Frank Lampard takes a shot. Blocked by Rafael Da Silva.
4:30 Assist on the goal came from Michael Carrick.
4:30 GOAL - Javier Hernandez:Man Utd 1 - 0 Chelsea Javier Hernandez finds the net with a headed goal from inside the six-yard box. Man Utd 1-0 Chelsea.
0:35 Rio Ferdinand fouled by Demba Ba, the ref awards a free kick. Rio Ferdinand takes the direct free kick.
0:00 The match has kicked off.
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