United were ahead after just 65 seconds when Wayne Rooney volleyed Nani's deflected free-kick high into the net for the away goal that boss Sir Alex Ferguson was craving.
However, Bayern responded well and eventually broke through when Franck Ribery's free-kick was deflected past the helpless Edwin van der Sar off Rooney. Gary Neville gave the free-kick away with a handball.
Ivica Olic then scored a late winner to complete Bayern's comeback and a measure of revenge for the 1999 final win for United. To make things worse for United Rooney limped off late on with an ankle injury, and Bayern proved Sir Alex Ferguson's side do not have the monopoly on memorable finishes.
Even before there was a full minute gone by Nani was floored by Martin Demichelis near the corner and the Portuguese winger floated free kick eventually found Rooney. He could hardly have believed that dead centre of the goal and only five yards out there was not a German marker within touching distance as he connected with a volley.
Bayern are still traumatised by the memory of those final minutes in the Nou Camp in 1999. But if they were suckered into believing that United still only specialise in late comebacks this early hit rocked them to the core.
Ribery's early heavy and nervous touches were of a man who realised the burden of being Bayern's great hope had taken on a major new level of importance.
But once he got stuck into the task United began to understand just why the early breakthrough had been so vital. Ribery danger
In fact had Ribery been surrounded by an attack anything near his quality the Reds could have had their lead wiped out midway through the first half.
Ribery's class opened up the Reds when he lifted a superb pass over United's defence but Altintop, who was worryingly in the clear, showed a dreadful touch to allow the Reds to escape.
Ribery then put United in panic mode again from a cross and this time it was Olic who failed to display a top class striker's awareness and reacted late to a loose ball.
They might have been comforted to note it happens to the best of the bunch as well because Rooney had a golden opportunity to grab a second.
After 39 minutes the human dynamo Fletcher put in a cross from the left and Rooney controlled only yards from goal but stabbed his effort at the legs of Bayern keeper Butt.
It was ultimately to prove a critical miss as Bayern finally found Louis Van Gaal's so-called level one form in the second half.
The German's coach had called his former Ajax keeper Edwin Van der Sar a made goalkeeper when asked about United's number one in the pre-match press conference.
Nobody in the United camp cared whether he was a natural or manufactured as he kept Bayern at bay single handedly as United were forced to defend for their lives.
Olic, Altintop and Van Bommel were all left frustrated by the Dutch giant.
But he couldn't do anything about the Bavarian's equaliser.
After Gary Neville had handled in the 77th minute Ribery sent in a free kick that took a deflection to beat Van der Sar. And with just seconds remaining on the clock, Olic pinched Patrice Evra's pocket, sped past Rio Ferdinand and finished well to exact Bayern's revenge. Rooney could only watch the goal from the floor having turned his ankle over and he limped off to complete a miserable night for United. What is your verdict on the action? Have your say.