United looked to be cruising to victory when Cristiano Ronaldo double and goals from Michael Carrick and Nemanja Vidic put them 4-1 up.
Sir Alex Ferguson brought back Rooney for Carlos Tevez and Van der Sar and Gary Neville were also back in the starting line-up.
And United were ahead inside just three minutes when Ronaldo rounded off a neat one-two with Dimitar Berbatov.
The Portuguese star is firmly back on the goal trail - hitting another double to follow up his brace against West Ham in midweek as he tries to emulate his incredible 42-goal campaign last season.
Rooney's near post was missed by Rio Ferdinand but Vidic did not as he steered home a side-footed shot from six yards. United were playing well but when Ferdinand hauled back Mendy and Geovanni converted the penalty, they were suddenly in a precarious position once more.
United: Van der Sar, Neville, Ferdinand, Vidic, Evra, Ronaldo, Carrick (Giggs 72), Anderson (O'Shea 88), Nani (Tevez 64), Berbatov, Rooney. Subs not used: Foster, Park, R. Da Silva, Fletcher.
Booked: Rooney and Tevez.
Goals: Ronaldo 3, Carrick, 29, Ronaldo 44, Vidic 57.
Referee: Mike Dean.
Man-of-the-Match: Cristiano Ronaldo.
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