كتب : Sherif Tarek
Paul Scholes opened the scoring when he volleyed Michael Carrick's corner-kick on 12 minutes, and five minutes later Dimitar Berbatov tapped in the second for the home side.
Rooney, who was nursing a hamstring injury for nearly a month, marked his comeback and put the icing on the cake from close range seconds after being introduced on 61 minutes.
Defending champions United are now five points ahead of their closest rivals Liverpool, who have 54, while Fulham remained in 10th place with 30.
Berbatov was about to notch his second one minute after tucking in, but he had his shot cleared off the line.
The Bulgarian ace also had a headed goal disallowed after being ruled offside late in the first period.
Throughout the game, Fulham were completely helpless and couldn't cope with United's persistent onslaught.
They only got one clear-cut opportunity when Bobby Zamora tried his luck on 66 minutes, but his effort drifted wide of the mark.