Despite hitting the woodwork on four occasions, it looked as though the visitors were going to have to settle for a share of the spoils at Craven Cottage until Rooney intervened.
Below, Sports Mole has looked back over the action to determine if Fulham deserved at least a draw.
On target 8
On target 8
Was the result fair?
Everybody connected with Fulham will feel that they deserved a draw from tonight's match and you can see why. They created chances and having fallen behind, they put United under some real pressure. However, football is all about taking your chances and the visitors eventually did that. It was a game of two halves really, but United created the more clear cut chances.
In all honesty, Fulham could not have performed any worse today than they did at Old Trafford last week. In fact, they were much better all round today. They defended well and when called upon, Mark Schwarzer did well with the gloves. Granted they rode their luck at times, after all United hit the woodwork on four occasions, but they were a match for their opponents for large parts. Overall, though, Martin Jol must have seen enough to have been content with his players.
Man United's performance
It wasn't always pretty, but manager Sir Alex Ferguson won't care one jot. That is the sort of victory that wins Premier League titles. United were comfortable the better side during the first half and during the second half when they came under pressure, they defended well.
Sports Mole's man of the match
Rio Ferdinand: He may have not had much to do during the opening 45 minutes, but after the restart United defender Ferdinand was called into action on numerous occasions. His positioning and reading of the game to snuff out dangerous attacks was impressive throughout. It's hard to see why Roy Hodgson does not include him in the England squad.
On one of the occasions United hit the woodwork, Patrice Evra should have done a lot better. The ball dropped to him six yards from goal, but he seemed to panic and only succeeded in lifting the ball onto the crossbar.
An easy evening really for Kevin Friend, who barely had a major decision to make. His most challenging moment arrived when the lights went out for a few minutes and he had to lead the players off the pitch.
Fulham: The Whites are on the road next Saturday when they travel to Norfolk to take on Norwich City.
Man United: A day later United will play host to David Moyes's Everton at Old Trafford.