For the second season running, the west Londoners made a win over the Premier League champions look more than easy.
A brilliant third from Damien Duff after 75 minutes as he placed a low left-foot drive past Tomasz Kuszczak, courtesy of a neat chest and lay-off from Bobby Zamora, sealed a lacklustre United's fate.
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Just 20 seconds into the second half, Zamora rifled in a close-range effort started by Duff and finally set-up by a header from Clint Dempsey.
As if a Scouser needed any invitation to score against Manchester United, Michael Carrick made it even easier for Danny Murphy to open the scoring on 17 minutes.
The stand-in defender stood off Murphy making his mind up for him as he let fly from 22 yards.
It still seemed as if Kusczak would be favourite to the low right-foot drive, but a combination of wicked bounce and the slightest of stumbles from the keeper saw the ball nestle nicely into the bottom corner
But what Paul Scholes was thinking as he casually turned on a poor pass from Darren Fletcher is anyone's guess.
Murphy easily robbed the midfielder to set up the chance in the first place.
In fact, an unfamiliar three-man United defence looked as if they had met each other for the first time in the Craven Cottage tunnel before kick-off.
Zamora should have added to his impressive recent haul but his header wide from six yards at the back post on 33 minutes after another fine piece of interplay involving Dempsey and Zoltan Gera's neat cross came to nothing.
Gera himself brought a great left-handed save from Kuszczak earlier as Zamora turned provider with a neat chest into the Hungarian's path. But although the first-time shot had power, it was also at the right height for the keeper to turn over.
At the other end, United's attack was giving Mark Schwarzer fielding practice.
A series of lofted and long-range efforts fell gratefully into the Aussie's arms - and none was more frustrating for the red army packing the Putney End than Wayne Rooney's 30-yard attempt that was closer to the middle of the stand than the goal in front of it.
Scholes' woeful first-half was summed up when he was rightly booked for a late challenge on Duff.
And although United switched to a 4-2-4 formation after the second goal went in at the other end - even with sub Dimitar Berbatov alongside Rooney - they were met by a stubborn white wall.