Manchester United are still on for a treble, while in under a fortnight Arsenal have gone from fighting on four fronts to concentrating on the league, if that hoariest of euphemisms may be permitted. If Arsène Wenger's players concentrate really hard they still have an excellent chance of denying United the title, though this FA Cup defeat was an immense psychological blow. Not only did United win as if the blip of the past couple of weeks had merely been a bad dream, they did so with a much-changed, almost unrecognisable side.

In all of Sir Alex Ferguson's battles with Arsenal and Wenger down the years, this victory was one that felt like a straight knockout, even if the visitors could justly claim that only Edwin van der Sar kept them out. "We could have won it by a few more, but they had chances too," Ferguson said.

"There was not that much in it, but after the major changes that were forced on us we can be well pleased with the result. I had to come up with a plan to utilise what energy was available, so I picked the players I knew would be keen and enthusiastic."

Arsenal turned up with quite a decent team despite their injuries, while United's lineup had everyone scratching their heads wondering where all the full-backs would fit in. Considering Arsenal famously failed to manage a shot on target in their last match, it was odd to see Ferguson name no fewer than seven defenders in his outfield lineup.

United started the game with only Wayne Rooney, Javier Hernández and Darron Gibson as recognised attacking players. Rooney was deployed in midfield with Hernández on his own up front.

While Ferguson had intimated in his programme notes that something needed to change – "We will need to snap out of our present form if the league match at the Emirates in May is to matter" – this seemed a bit drastic, as if the real United were being saved for Marseille on Tuesday. Didier Deschamps, watching from the stand, will not have learned much about United's likely Champions League formation, but will have formed a similar impression to his Arsenal counterpart about their fighting spirit.

"We were not outplayed, but United are always strong on the counterattack and clinical in front of goal," Wenger said. "It was a strange game, we put in a lot of effort and got nothing. Now we need to respond quickly and win our next games."

Arsenal will have to do that without Johan Djourou, who is out for the rest of the season with a dislocated shoulder. At least Arsenal registered their first shot on goal here after only three minutes, though Van der Sar was barely troubled by Andrey Arshavin's tame effort.

United showed their potency 10 minutes later when the Da Silva brothers combined to create a real chance but, after good work by Gibson, Rafael's header from Fábio's excellent cross went wastefully over the bar.

Arsenal should have taken notice, for the two Da Silvas combined again in the build-up to United's opening goal. In fact, the twins made a pretty good case for being selected in midfield more often. Fábio began the move on the right, found his brother, then from Rooney's well-flighted cross Hernández tested Manuel Almunia with a firm, deliberately placed header. The goalkeeper kept it out but could neither hold the ball nor steer it to safety, leaving Fábio with a tap-in for his second goal for the club.

As if to emphasise their strength in depth, United brought on Antonio Valencia after a six-month absence in place of their goalscorer for the second half and quickly increased their lead.

It was another calamity of sorts in the Arsenal defence, Djourou doing well to block a Hernández shot from Rafael's cross but then watching helplessly as the ball spun up for Rooney to head into the corner of an unguarded net.

Neither of the goals that Arsenal conceded were howlers of Carling Cup final proportions, yet on both occasions United prospered simply by having men in forward positions to tuck away loose balls in the six-yard area. When Samir Nasri hammered in a stinging shot a couple of minutes after the goal Van der Sar had to show sharp reactions but still caught it cleanly.

Marouane Chamakh also tested the goalkeeper with a forceful shot shortly after coming on. He too found the ball stuck. But the substitute had a better chance from Bacary Sagna's cross before the end. This time Van der Sar could only manage a fingertip save and the ball came back, but Wes Brown tidied up, as did Nemanja Vidic when Van der Sar parried another Chamakh shot.

Arsenal's luck was summed up when Almunia produced a scrambling save to prevent Hernández adding a third goal when Ryan Giggs and Rooney launched a breakaway, only for the influential Djourou to injure himself trying to get back, leaving Arsenal to see out the game with 10 men.

Their hopes for the rest of the season cannot now be high, whereas United have a new spring in their step. Even their manager has rediscovered his combative instinct, though not as much as the fractious Paul Scholes, who was lucky to stay on at the end and will miss United's next two league games after being booked for a foul on Chamakh.

Once Marseille are out of the way, Ferguson can't wait to take on the FA. "I don't think sticking up for my team makes me a villain, especially when you consider that Manchester United have one of the best disciplinary records in the country," Ferguson said. "I will defend myself strongly when my hearing comes up, in fact I am looking forward to the challenge.

"To my mind I have not said anything out of place, I thought my players performed well at Chelsea and were undone by decisions that went against them. I said as much and now I am facing a charge for telling the truth. I was disappointed with Graham Taylor, who wrote that I had to take the rough with the smooth. I remember him when he was England manager complaining to a linesman that the referee had got him the sack."