Blackburn survived the early sending-off of Yakubu to climb out of the relegation zone for the first time since September with a valuable win.
Striker Yakubu saw red midway through the first period for a recklessly high challenge on Danny Murphy.
But the home side went ahead through Morten Gamst Pedersen's curling free-kick before David Dunn's low shot.
Damien Duff fired in for Fulham but Mauro Formica completed victory with an excellent late third.
The three points sees Rovers climb up to 17th in the table and offers the prospect of some respite for under-pressure manager Steve Kean.
Kean has come under attack from sections of the home support all season and some against the club's owners outside Ewood Park before kick-off.
Without the formidable presence at the back of captain Chris Samba, who was reportedly suffering from illness but who stated this week that , the home side were slow to settle and Bobby Zamora could have headed Fulham ahead when he struck the post from 10 yards.
Yakubu was then dismissed for a crude challenge as he competed with Murphy for a bouncing ball, the Nigerian striker catching the former England man well above his knee.
Kean and Yakubu were furious at the decision but the striker - who has scored 13 goals this season - now faces a damaging three-match ban.
David Goodwillie was introduced up front as Blackburn looked to pose a threat on the counter, and for all their possession Fulham failed to make their man advantage count.
Zamora was close to getting on to the end of a John Arne Riise cross before Philippe Senderos was denied by a superb save from Paul Robinson.
Rovers took the lead in first-half stoppage time when Dunn won a dubious free-kick when he was sandwiched between two challenges, and Pedersen was able to fire the ball into the bottom corner from the edge of the box.
Kean's side then shocked Fulham by doubling their advantage inside a minute of the restart.
Dunn played the ball into Goodwillie inside the box, and when his shot was blocked by Riise, Dunn cracked home from just inside the area.
Fulham finally upped their game and had a Clint Dempsey effort disallowed for offside as he headed in Riise's free-kick before Duff struck against his former club.
The Republic of Ireland winger collected Murphy's pass on the right of the area and was allowed to shoot through Martin Olsson's legs and into the far corner.
Blackburn - without a home win since Yakubu struck all four past Swansea at the start of December - could have crumbled, but to their credit they began to take charge of the game.
The impressive Junior Hoilett went close to a third but his shot was saved by David Stockdale, while the busy Steven Nzonzi and Pedersen nullified any Fulham threat with excellent performances in midfield.
Fulham boss Martin Jol brought on Andrew Johnson - reportedly a transfer target for Rovers - but it was the home side who again threatened when Goodwillie shot wide.
And the hosts got the third goal their second-half showing deserved when Nzonzi lofted a clever pass over the top of a square Fulham backline, substitute Formica letting it bounce before dispatching a left-footed half volley across Stockdale and into the net.
Fulham manager Martin Jol:
"We knew before the game Blackburn would fight for their lives but after the first half-hour we were the better team.
"At 2-0 down it was difficult but with our offensive quality I thought we would at least get a draw.
"They played with a lot of energy and we struggled to close them down."