The United number 10 was quick to convert one of United best chances of the first half, as Jonny Evans headed an Ashley Young’s cross back into Rooney’s path.
The result sees United moving three points clear of City but United were made to sweat for the result, as Fulham saw their appeals for a penalty waived away minutes from time after Danny Murphy was challenged in the box by Michael Carrick.
United looked to make the make the most of Citu’s slip up against Stoke and set out with an attacking line up that included Rooney and Welbeck up front, with Giggs, Valencia, Young and Carrick in midfield.
Rafael, Ferdinand, Evans and Evra were chosen to protect DeGea.
United started well and Fulham barely touched the ball in the first ten minutes, even though they went close to opening the score, as Dembele fired his shot wide.
DeGea was then tested by Dempsey twice, as the Spanish goalkeeper continued to show his fine form.
United, who had been largely subdued, had their first real chance as Evra’s overhead kick went narrowly wide, while Rafael saw his shot parried by Schwarzer.
United had their breakthrough when,following Ashley Young’s cross, Evans pulled the back for Rooney who hammered it back home from close range for his 17th goal in his last 17 games.
The second half saw United creating a few good chances, mainly through Antonio Valencia and Ashley Young, but Schwarzwer brilliantly denied both United wingers, keeping Fulham in the game.
The Fulham keeper produced two outstanding saves as he kept out Ashley Young’s volley and follow-up, before Hangelaand cleared Ryan Giggs’s goal bound effort.
Hernandez and Smalling replaced Welbeck and Ferdinand, while Scholes came on for Rooney, but United looked happy to keep the possession instead of killing the game off.
And they almost paid the price for that, as Carrick clipped Danny Murhphy inside the box but the referee waved play on.
It wasn’t a pretty win for United, but a win nonetheless, and this kind of result could well be the difference between Fergie’s men and the noisy neighbours in May.