Rooney, who replaced ineffective Bulgaria forward Dimitar Berbatov at halftime, was shown the red card in the 88th minute after hurling the ball in the direction of referee Phil Dowd.
United finished with nine men after Paul Scholes was sent off for a handball on the line after 18 minutes with Danny Murphy scoring the resulting penalty to put Fulham ahead.
"The ball was thrown to where the free kick was being taken -- did it hit the referee? No," Ferguson told MUTV after his side's first back-to-back defeats in the league for four years.
"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.
"In the first half we never got started."
United assistant manager Mike Phelan earlier described Rooney's red card as an over-reaction by the referee.
"It seemed very trivial -- not in the referee's eyes, but in our eyes. It was a trivial thing to do," he told the BBC.
United were let off the hook by second-placed Chelsea's defeat at Tottenham which ended manager Guus Hiddink's 100 percent start in the league since taking over last month.
However, Liverpool can cut United's lead to one point if they beat Aston Villa at Anfield on Sunday.
Chelsea would have moved within a point of United with a win at Spurs but were beaten by a Luka Modric goal -- a defeat Hiddink said could scupper the west London side's hopes of stopping United winning a hat-trick of league titles.
"These are the days you look back on and regret very much when you are in a title race," Hiddink told the BBC.
"We won't give up on the title but today was an ideal opportunity to close the gap on Manchester United and we missed it. We cannot afford to drop two or three points in any game if we want to catch United, and today we lost -- it's a huge blow."
The Premier League breaks off for international duty next week and Fergsuon hopes his side rediscover the form that took them on an 11-match winning league run recently and put them in sight of a record-equalling 18th English crown.
"If you lose games in March and April it can cost you," said Ferguson, who this week described title run-ins as agony.
"Fortunately we have a slender lead at the moment but not a lot and I'm hoping we come back from the internationals back to our best."
Nemanja Vidic, Scholes and Rooney are all suspended for their next league game at home to Aston Villa on April 5 while Berbatov suffered an ankle knock that adds United's worries.
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