The champions scrambled to victory at Old Trafford to open up a three-point lead at the top of the Premier League.
Rooney's 28th goal of the season proved enough for the hosts.
Sir Alex Ferguson was clearly not impressed though and his side were nearly made to pay the ultimate price for their profligacy when Michael Carrick bundled Danny Murphy over in the box a minute from time but 27-year-old referee Michael Oliver waved away the penalty claims.
Having witnessed title rivals Manchester City drop points at Stoke on Saturday, Ferguson had gone for the jugular with his team selection.
Five offensive players and two naturally overlapping full-backs was a ploy designed to push Fulham onto the back foot, and so it did as Rooney and Ryan Giggs threatened the visitors' goal.
Fulham eventually emerged from their shells though and started to exploit the gaps being offered.
Mousa Dembele drove one effort wide after being invited to run at the United defence, then Clint Dempsey had a go.
The American is much more dangerous and as he set his curling shot for the corner, Fulham's 320-strong travelling support were ready to celebrate.
It was too good to be true though for a team that had only beaten United once away from home since 1959, and David De Gea made an acrobatic save.
From that moment on, the Red Devils exerted their customary pressure.
Their play was not fluent though. A long-range Danny Welbeck shot and a penalty appeal for handball against Stephen Kelly was the best they could muster until Rooney struck.
Even that was a touch odd.
Rooney ducked under Ashley Young's cross when he seemed better placed to convert than Jonny Evans behind him. John Arne Riise should have cleared but it seemed the Norwegian was surprised by Rooney's move and he failed to control, allowing Evans to slide in. The Northern Irishman had the presence of mind to find Rooney instead of going for goal himself from an acute angle.
From that moment, Fulham were doomed as Rooney rattled home his 11th goal in nine games.
If there is one player who has been as influential as the England striker since the turn of the year, it is Antonio Valencia.
Not even a month on the sidelines with a hamstring injury has affected his form and he came close to bagging a brilliant second goal just after the interval.
Setting off on a charge from deep inside his own half, Valencia exchanged passes with Rooney on halfway before squaring to Ryan Giggs and running onto the veteran Welshman's chipped return. Now Valencia was bearing down on the Fulham goal but Mark Schwarzer stayed strong and made the save
Yet for all the simplicity of that effort, United found chances hard to come by against Fulham's disciplined defending.
Javier Hernandez was introduced to give the visitors a different problem to solve but United's next opportunity was quite a while coming, and when it did, Giggs dragged it wide.
Having spoken in such glowing terms about Rio Ferdinand in the build-up, the veteran defender's exit 20 minutes from time was a worry given his long-standing back problems.
United should have made light of his departure by grabbing a second soon afterwards but Schwarzer produced a fine save to repel Young's volley, then kept out the follow-up too before Brede Hangeland prevented Giggs from converting.
In replacing Rooney with Paul Scholes, United seemed to be insuring themselves against unexpected disasters against a hitherto non-existent attacking threat.
But it was the veteran midfielder who put his own team under pressure with a pretty awful tackle on Dempsey that was fortunate to escape sanction beyond a simple free-kick.
Normally content to watch proceedings from the dug-out, Ferguson was clearly agitated and unimpressed by his side's performance.
The Scot really would have been furious had Oliver awarded a penalty for Carrick's tackle from behind on Murphy in the final minute, which TV replays showed he had every right to do.