Nemanja Vidic's injury time header gave The Reds the edge after Horward Webb had ruled out an opener when Ryan Giggs floated over the corner that Berbatov flicked on.
The linesman ruled that the corner had not been taken properly, sparking furious protest from Rooney and Giggsy.
Chelsea began the 2nd-half brightly but United killed the game when Evra exchanged passes with Cristiano Ronaldo down the left and floated over a cross that just evaded Dimitar Berbatov and Ashley Cole seemed to have covered, only for Rooney to stick his leg out and turn the ball past a startled Cech.
And with three minutes left Dimitar Berbatov completed an emphatic victory by volleying home from Ronaldo's whipped free kick to the near post.
Team line-up: Van der Sar, Neville, Evans, Vidic, Evra (O'Shea), Ronaldo, Fletcher, Giggs (Carrick), Park, Rooney, Berbatov.
Booked: Ronaldo, Rooney.
Referee: Horward Webb
Man-of-the-Match: Nemanja Vidic.
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