The first red card of Ayegbeni Yakubu's nine-year career in English football midway through the first half seemed to add to beleaguered manager Steve Kean's woes.
But Morten Gamst Pedersen and David Dunn struck either side of the interval, and despite Damien Duff pulling one back, substitute Mauro Formica sealed only Rovers' fourth league win of the season.
QPR and Wigan still have to play this weekend, but the fact Rovers sit 17th after today's games will at least give Kean encouragement.
The latest fans' protest against owners Venky's outside the ground before kick off was but a sideshow, and completely forgotten about come the final whistle.
The fans, though, are having their say with their feet as just 18,003 turned up at Ewood Park, the worst league crowd for many years.
Those that stayed away, however, missed a rousing performance from Kean's side, who were spurred into action after Yakubu's dismissal.
Bobby Zamora had just planted a header on to the angle of bar and post from a Damien Duff right-wing cross when the complexion of the game changed, albeit in Rovers' favour.
Kean could be seen mouthing 'That's a disgrace' towards referee Anthony Taylor, but the Cheshire official brandished the red card.
In going for a loose ball with Danny Murphy, Yakubu was high with his right boot, and to add to his indiscretion his studs were showing, catching the Fulham midfielder on his right knee.
It means Rovers will be without their leading scorer for the next three matches, all in the league against Everton, Newcastle and Arsenal, with the middle fixture of those on home soil.
Despite that, it was Rovers who went into the break with the lead, and perhaps rightly so as Fulham showed little invention with the extra man.
Zamora did come within inches of turning home a low ball into the six-yard box from Moussa Dembele, and Paul Robinson made a superb save six minutes from the break.
That saw the England international at his best in clawing away a goal-bound header from Philippe Senderos after the defender was allowed to rise unchecked on to a free-kick from Murphy.
But in the fourth minute of injury time Pedersen stroked home his third goal of the season, curling a low 20-yard free-kick beyond the outstretched grasp of David Stockdale after Bryan Ruiz had brought down Dunn.
If Martin Jol had given his players a roasting during the break, it had virtually no time to sink in because just 56 seconds into the second half Blackburn doubled their lead.
Steven Nzonzi's initial drive inside the area was blocked by John Arne Riise, however, the rebound fell to Dunn who struck a piledriver of a shot beyond Stockdale for his first goal since February 5 last year.
Fulham were finally roused, and four minutes later they thought they had pulled one back, only for Clint Dempsey to be narrowly flagged offside in heading home a save from Robinson who had initially palmed away a stinging effort from Riise.
Less than six minutes later, though, they were back in the game, and all too easily at that.
When Murphy played a pass out towards Duff, who was outside the area and 20 yards from goal at that point, there appeared to be no danger.
Duff, however, eased his way into the box and from an acute angle stroked a right-foot drive beyond a static Robinson for his fifth goal of the season, and second in successive games.
Rovers, though, should have restored their two-goal cushion in the 65th minute, only for Stockdale to beat away Junior Hoilett's 12-yard effort after being teed up by Pedersen.
With less than 20 minutes remaining Jol threw on Blackburn target Andrew Johnson for Riise, sacrificing a defender for a striker in a bid to salvage something from the game.
But in the 79th minute it was Rovers who grabbed the next goal with 69th-minute sub Mauro Formica beating Stockdale with aplomb from 12 yards after being played in by Nzonzi.