Sir Alex Ferguson's team had been knocked off top spot by Chelsea's victory against West Ham on Saturday, but Rooney struck 30 seconds after half-time at Old Trafford and added a second in the closing stages.
Dimitar Berbatov headed United's third goal in the last minute to ensure the champions moved two points clear of the Blues and third placed Arsenal.
United had lost 3-0 at Fulham earlier this season but Rooney, who has now scored 16 goals in his last 11 United appearances, broke their resistance when he met Nani's cross with a first-time finish that flashed past Mark Schwarzer from 10 yards out.
England forward Rooney put the result beyond doubt when he swept in Berbatov's 84th minute cross to take his goal tally for the season to 32 in all competitions.
Berbatov sealed the rout with a diving header from South Korea winger Park Ji-Sung's 89th minute cross.
Manchester City will aim to keep their challenge for fourth place on course at Sunderland in Sunday's late game.
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