A second-leg draw was good enough to send Crewe into the League Two play-off final at Southend's expense.
Leading 1-0 from the first tie, the Alex doubled their aggregate lead with AJ Leitch-Smith's fine finish.
Neil Harris pulled one back following Steve Phillips's fumble before Max Clayton once again extended the visitors' advantage.
In a frantic finish Chris Barker nodded home Ryan Hall's cross but it was not enough to stop Crewe reaching Wembley.
It was a true display of the lottery of the play-offs as Southend, who spent a large part of the season top of the league only to narrowly miss out on automatic promotion, were put to the sword by a Crewe side who were 12th when the two teams met in February.
That loss triggered a remarkable undefeated run for the Alex, who have now gone a club-record 18 games without tasting defeat.
And they took the lead at Roots Hall when Ashley Westwood won a battle with Anthony Grant in the centre of the park before releasing Leitch-Smith down the left. He showed the quickest of feet to cut into the area and send an arching drive beyond Belford.
Southend thought they had pulled one back when Freddy Eastwood snaffled the chance after Phillips had parried Hall's strike, but the Coventry loanee had roamed offside.
Crewe, exploiting the space as Southend continued to push forward, were handed plenty of chances to put the tie to bed.
Belford's mis-kicked clearance fell into Byron Moore's path, but he blazed over with only the keeper to beat and Leitch-Smith, who moments earlier had been harshly booked for diving, hit his effort tamely at the keeper when Lee Bell had chipped him through.
Finally the Southend fightback came and Crewe had both posts to thank for preserving their lead as Michael Timlin struck one and then Eastwood the other.
The breakthrough arrived moments later, with Phillips failing to collect Barker's cross and substitute Harris sweeping in the loose ball.
The joy was short-lived though, as Crewe's highly fancied youngsters Nick Powell and Clayton combined, the latter finding enough space under pressure to fashion a cute finish, which sneaked just inside the wrong-footed Belford's left upright.
Barker hit back late on, applying the finish to Hall's stunning chipped cross, but it was not enough to stop Steve Davis's men from continuing their march towards Wembley, where they meet either Cheltenham or Torquay.
VIEWS FROM THE DRESSING ROOM
Southend manager Paul Sturrock told BBC Essex:
"You can't play a game like we've tried to play, 45 minutes of football. If we'd shown that aggression and appetite in the first half, I think we'd have come out the victors.
"The biggest game of the season and we just didn't get to grips with the game at all. They were the eager team and got the goal they deserved.
"I think we shaded the second half, but the horse had bolted by then. I'm absolutely gutted for everybody involved with the football club."
Crewe Alexandra manager Steve Davis told BBC Radio Stoke:
"I'm delighted for everyone, the supporters and the staff, who have all worked very hard to get to this.
"It's a great achievement. And I'm proud of everybody. It's given everyone a lift.
"It was an exciting game and I'm delighted we came out on top. I hope everyone can make it to Wembley."