A volley executed to perfection by Arjen Robben 16 minutes from the end secured Bayern's passage after United had raced into a 3-0 lead on the night.
Ivica Olic brought Bayern back into contention in the 43rd minute and their cause was aided by United defender Rafael's dismissal for a second bookable offence five minutes into the second half.
"We were asleep at the start and Man U were superior in every aspect," admitted Beckenbauer.
"At 3-0, I would not have bet even a cent on Bayern. But they turned it around magnificently.
"Two moments were decisive: the goal for 3-1 from Olic just before the break and then Rafael's red card. Bayern then played with composure, let the ball roll and Robben then scored a dream goal.
"It was one of the most beautiful defeats in Bayern Munich's history."