United recorded their biggest away win in Europe since 1964 to make top spot in Group A their own on Matchday 5 and confirm progress to the Round of 16 with a stunning display against the Bundesliga's second-placed side.
Antonio Valencia opened the scoring on 22 minutes when Rooney produced a cross which the Ecuadorian tapped home before his dangerous free-kick forced Emir Spahic to head into his own net on the half-hour mark.
Defender Jonny Evans made it 3-0 in the 65th minute when he scuffed home a deflection which came courtesy of Rooney's initial effort before the England international set up Chris Smalling with a 77th minute lob.
The win has the Old Trafford club sitting three points ahead of Shakhtar Donetsk, who moved into second thanks to their 4-0 home win over Real Sociedad, while Bayer are a still a chance to qualify if they can beat the Spaniards in San Sebastien on December 10.
2013/14 UEFA Champions League - Group A scores
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