Damien Duff had given Fulham a surprise lead in the third minute, before the Netherlands striker met Patrice Evra's cross with a neat left-footed flick into the far corner of Mark Schwarzer's goal seven minutes later.
Shinji Kagawa also scored his first for United in the 35th and Rafael Da Silva added a third with a header, giving United a 3-1 lead at half time.
Nemanja Vidic's own goal in the 64th minute started a spell of pressure by the visitors, but they were unable to find an equalizer.
"I think we saw the two sides of Manchester United," Ferguson said. "''After cruise control, we made a terrible mistake for the second goal and it became a match."
Wayne Rooney went off on a stretcher in injury time with a deep gash after getting caught on the right leg by Hugo Rodallega, something that will sour the victory for Ferguson.
"It looks as he'll be out for maybe four weeks," Ferguson said.
In Saturday's late kick off, Eden Hazard and Fernando Torres combined to devastating effect as Chelsea beat Newcastle 2-0 at Stamford Bridge.
Hazard converted a penalty for his first Chelsea goal after Torres was fouled before assisting on the second with a back heel for Torres to score from 18 yards just before half time.
Chelsea now has three wins from three games prompting manager Roberto Di Matteo to praise the start his team has made.
"We controlled Newcastle's threat well," Di Matteo said. "With two clean sheets in three games, I am very pleased."
The same could not be said of Di Matteo's predecessor at Chelsea, Andre Villas-Boas, who came close to his first win as Tottenham manager but settled for a 1-1 draw with West Bromwich Albion.
Benoit Assou-Ekotto gave Tottenham the lead at White Hart Lane in the 74th minute before James Morrison saved a point for West Brom with a 90th-minute goal.
Villas-Boas refused to be concerned by the slow start Tottenham has made to its season.
"We are just waiting for the results to accompany us a little bit more," Villas Boas said. "Now we just have to be a bit more aggressive in front of goal. We have to finish the chances we have."
West Brom manager Steve Clarke nearly substituted his goal scorer Morrison during the game after he rolled his ankle in only the second minute of the game.
"We weren't sure whether he would continue," Clarke said. "It did cross my mind to bring him off a couple of times, but you have to leave someone like James on the pitch because he can pop up with a goal and he did that."
Everton beat Aston Villa 3-1 at Villa Park, with Steven Pienaar, Marouane Fellaini and Nikica Jelavic all scoring before half time.
Villa had Ciaran Clark sent off in the 58th before Karim El Ahmadi scored a consolation goal for the home side.
David Moyes refused to say he has been surprised by the start his side has made to its Premier League campaign after following up a 1-0 win over Manchester United with victory over Villa.
"I am not surprised because I think we have a good team," Moyes said. "Can we keep them all fit? Can we play as well as we did today? Those are the questions, but when we do we are a match for most teams."
Norwich and Queens Park Rangers drew 1-1 at Carrow Road in a fixture featuring two teams that were beaten 5-0 last weekend.
Simeon Jackson of Mississauga, Ont., put Norwich ahead on 11 minutes but Bobby Zamora pulled his side level, converting the rebound after Djibril Cisse's penalty was well saved by John Ruddy.
Federico Di Santo and Arouna Kone's second-half goals secured three points for Wigan away at Southampton. Earlier Saturday, Michael Laudrup's Swansea beat West Ham 3-0 in a dominating display, thanks to goals from Angel Rangel, Michu and Danny Graham.
Sunderland's home fixture against Reading was postponed due to a waterlogged pitch.