For not only does the loss, on the back of the crushing home defeat to Liverpool, now give Rafa Benitez's side the opportunity to close the gap at the top to just one point if they can beat Aston Villa at Anfield today.
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Manchester United manager Sir Alex Ferguson bemoans title slip-up
It also means United, who had not lost back to back games for 147 matches, will now lose both Scholes and Rooney for their own crucial encounter with Villa after the international break.
The only good news on a wretched day for Ferguson was Chelsea's failure to narrow their own four point deficit by losing at Tottenham.
"If you lose games in March and April, it will cost you," admitted Ferguson. "We still have a slender lead but not a lot. The disappointment for me is that we didn't get a response after the Liverpool game."
The idea that a hair dryer must have been blowing on the banks of the Thames was given credence when Ferguson suggested "there was some talking done at half-time" after United had been outclassed before the break by a team they had hammered here 4-0 just a fortnight ago.
But Ferguson was unhappy with both the sendings-off by referee Phil Dowd.
Scholes handled on the line, allowing Danny Murphy to give Fulham the first-half lead from the spot, but Ferguson felt the official could have spared his veteran. "But that's Phil Dowd for you," he complained.
Rooney was dismissed for a second yellow when he threw the ball down the pitch after a decision went against him but Ferguson was adamant that, though the England striker had acted "in anger", he had only hurled the ball back to get play restarted quickly.
"The ball was thrown to where the free-kick was being taken. Did it hit the referee? No," said Ferguson. "But there's no point talking about the referee. We didn't play well enough in the first half and that's why we lost."
Delighted Fulham boss Roy Hodgson reckoned: "We've opened up the title race. But if you ask me, I still think United will win it."