Rooney's 10th goal in as many games 11 minutes from time sent United 10 points clear of Manchester City, who entertain Liverpool tomorrow, and a massive 16 ahead of third-placed Chelsea.
And it all came after a whirlwind opening was halted by a break in play just before half-time when the stadium was plunged into darkness.
Prior to that, United had struck the woodwork on three occasions, and Fulham once.
But instead of a goal deluge, there was just Rooney's single strike, a cool curling finish from David De Gea's long punt downfield.
Released from the Old Trafford cabbage patch, United stated their intent by selecting two orthodox wide-men and attacking from the first whistle.
With Fulham, even minus former Red Devils striker Dimitar Berbatov, far more of a threat than they were when the sides met in the FA Cup seven days ago, it made for a rip-roaring opening in which both keepers excelled and the woodwork at either end was rattled.
Indeed, in more ways than one, the mad penalty box scramble after nine minutes proved to be a sign of things to come.
Robin van Persie's corner started it, bouncing off Brede Hangeland and towards his own goal, forcing Mark Schwarzer into the first of a series of excellent saves.
Patrice Evra reacted quickest but could only scoop the ball against the bar before Sascha Riether cleared Wayne Rooney's shot off the line.
United maintained the pressure but Schwarzer came to Fulham's rescue again with another fine stop to prevent Evra's effort flying in.
Within seconds, John Arne Riise tested De Gea with a dipping effort the under-fire Spain youngster tipped over.
De Gea got nowhere near a Bryan Ruiz shot that thudded against a post before play switched down to the other end where Hangeland, after denying Nani with a superb last-ditch tackle, turned Van Persie's corner on to the bar.
Only then did a breathless contest slow in intensity, although a brilliant move involving Nani and Tom Cleverley created another opportunity for Rooney, which he stroked against a post.
Nani was certainly making an impression on only his fourth match back after two months out with a hamstring injury, only for his momentum to be halted as the stadium was plunged into darkness.
The players did return to complete the opening period, although Van Persie's shot, gathered at the second attempt by Schwarzer, was the only incident of note.
So brilliant has Van Persie been for United this season it is a disappointment when he has a quiet game.
This one went on around him after the re-start, a failure to get any power behind a header from Nani's cross his only opportunity of note.
Indeed, the floodlight incident seemed to take the zip out of the entire contest, with neither side coming close to matching the thrills they had produced before the impromptu break in proceedings.
Van Persie did somehow wriggle his way down the by-line before setting up Nani, only for Chris Baird to block.
De Gea endured another uncomfortable moment when he could only parry Riether's shot to Bryan Ruiz, but the Fulham forward was unable to get any purchase on his volley.
For a while it appeared Fulham might claim a major scalp.
Rafael cleared off the line from Ruiz after Jonny Evans had been forced to head away from underneath his own bar.
Rooney had other ideas, though, and when Fulham failed to get a touch to Evans' long kick downfield, the England man picked his spot and, in front of England manager Roy Hodgson, calmly found the bottom corner.
Van Persie might have added a second only to volley over from close range, although the striker was required at the other end to clear Philippe Senderos' injury-time header off the line.