The England striker struck twice in the second half to hand the home side victory, with the Uruguayan's return not enough to help the Reds make up ground on the top four
Tensions ran high in Manchester, as Luis Suarez returned to the Liverpool starting XI for the first time since he was suspended for racially abusing United defender Patrice Evra – refusing to shake the Frenchman's hand before kick-off – to poach a late consolation goal for the visitors.
Rooney, though, stole the show, as his two goals early in the second half proved enough to hand United three points and send them top of the Premier League table, with Manchester City still to play on Sunday.
Sir Alex Ferguson made only one change from the side that drew 3-3 with Chelsea, as Ashley Young dropped out of the squad altogether. Paul Scholes replaced him in midfield, with Ryan Giggs shifting to the left-hand side. United were, however, boosted by the return of Tom Cleverley to the bench.
Suarez, as expected, was made to feel decidedly unwelcome at Old Trafford but Kenny Dalglish had no hesitation in throwing the Uruguayan striker back into the Liverpool attack. Andy Carroll and Craig Bellamy were among the substitutes, with Jordan Henderson returning to the midfield ahead of Charlie Adam.
All eyes, as has become the custom following player feuds, were on the pre-match handshakes and Suarez did nothing to cool tensions ahead of kick-off by refusing to acknowledge Evra. The 25-year-old was then snubbed himself by Rio Ferdinand.
With the pre-match niceties, or lack of them, out of the way, the game itself began at an encouraging pace. Antonio Valencia immediately began to cause Jose Enrique problems on the United right, but without a genuine left winger to mark, Liverpool right-back Glen Johnson looked the most threatening player on the pitch in the opening exchanges. The English defender cut inside Evra before shooting narrowly wide from the edge of the box.
Giggs began the game tucked in alongside Scholes and Michael Carrick, but as he was forced wider to counter Johnson, Liverpool began to get more of a grip on the match in central midfield. Despite Giggs' troubles, he did find the space on the left after a tremendous United move to cross on to the head of the unmarked Scholes, who was denied at point blank range by Pepe Reina.
By the end of the half, Suarez was once more the focus of Old Trafford. After complaining furiously that he was fouled by Ferdinand when through on goal – replays showed the 33-year-old won the ball – the striker, in his frustration, booted the ball towards the stands as Phil Dowd blew his whistle for the break.
That antagonism reportedly spilled over into physical confrontation as the two teams made their way into the dressing room, but the second half started in explosive fashion for footballing reasons.
Giggs' corner from the United right-hand side was inadvertently flicked on at the near post by Jordan Henderson into the path of Rooney, who volleyed beyond Reina from close range to open the scoring.
He wasn't finished there. Jay Spearing was hounded down by Valencia around the edge of his own penalty area and after the Ecuadorian had turned over possession, he was left with the simple task of rolling a pass into the path of Rooney, who passed the ball into the back of the net to leave Liverpool reeling.
Rooney should have had his hat-trick by the hour mark. After Scholes smartly dummied Valencia's pass across the edge of the penalty area, the 26-year-old advanced on to Reina only to poke the ball wide of goal from little more than eight yards out.
Dalglish introduced Carroll and Bellamy in an attempt to revive his side's chances but whereas Johnson had rampaged into space in the first half, Rooney was the man enjoying the freedom of Old Trafford in the second. David de Gea remained largely untested through 75 minutes as Adam joined the fray for the visitors.
United were looking comfortable until an innocuous free-kick into the penalty area was miscontrolled by Ferdinand, allowing Suarez to bring the away team back into the game from inside the six-yard box.
De Gea saved well from Johnson but United were able to hold on to ensure that the Reds continue to trail Chelsea, Newcastle and Arsenal in the race for a place in next season's Champions League.