Rooney took his tally to 21 for the season as his contribution once more proved invaluable to his side, who fully exploited title rivals Manchester City’s slip up at Stoke on Saturday.
Some poor defending from Fulham allowed the reigning Champions to open the scoring with 41 minutes on the clock.
John Arne-Riise’s failure to deal with a ball into the area allowed Jonny Evans to poke the ball to Rooney lurking in the six yard box to make it seven in his last six games.
Fulham were left ruing their defensive slip up as it proved to be the difference in a game they could quite legitimately claim to have deserved at least a point from.
Both Clint Dempsey and Kerim Frei were causing problems for the home side, with the American curling a shot over from 25 yards as an early statement of intent.
United were seemingly struggling to get going, although Antonio Valencia’s charge in the box and subsequent shot which was blocked by Riise hinted at the Champions rumbling into life.
Fulham were aggrieved as Rooney pounced to put United up with just four minutes remaining, and that goal appeared to jolt the home side into life as they emerged in the second half much the better side.
Valencia had another good effort saved excellently by Mark Schwarzer after Ryan Giggs, earlier booked for a mis-judged lunge on Moussa Dembele, played a well weighted ball over the top to the Ecuadorian.
Schwarzer was starting to be tested more regularly as Ashley Young shot from distance forced him into action before Danny Welbeck found space in the area but saw his effort blocked before it could make its way through to the Australian.
In control of the game, United boss Sir Alex Ferguson would have been concerned at the sight of Rio Ferdinand limping off to be replaced by Chris Smalling, while the Scot's decision to remove Rooney from the fray with 12 minutes left was not forced upon him but raised as many eye brows.
Fulham found some breathing space in the final stages of the match and came forward in search of an equaliser, but were denied a certain penalty in what is likely to be the game’s main talking points in the days to come.
With the 90 minutes up Danny Murphy found space in the box and was clumsily bought down by Michael Carrick, only for referee Michael Oliver to wave play on much to the annoyance of Cottagers boss Martin Jol with the final whistle following soon after.