Two goals in the final 14 minutes from Franck Ribery and Ivica Olic helped Bayern gain revenge on United following their dramatic Champions League Final defeat at the Camp Nou back in 1999.
However, of more concern to United and England fans was the sight of Rooney being helped off the pitch at full-time having taken a blow to the ankle in the build-up to Olic's stoppage-time winner.
The night had started perfectly for United as they swept into a second minute lead in the first leg of their last eight encounter at the Allianz Arena.
Rooney profited from a slip by Martin Demichelis to side-foot a simple finish into the roof off the net after Nani's free-kick flicked off the head of Mark van Bommel.
But that was as good as it would get for the visitors as they failed to match Bayern's intensity and were lucky to go in level at half-time.
First Ribery's left-foot shot from the edge of the box was held superbly by the diving Edwin van der Sar, before Hamit Altintop inexplicably mis-controlled when free in the box and he failed to capitalise on a sensational chipped pass from the lively France star.
Olic wasted the best chance on the half-hour when he thrashed at fresh air and made a hash of Altintop's shot which came to him just three yards out.
The Croatia striker tested van der Sar at the base of his post in the opening stages of the second half before Altintop drew a fine save from the busy Dutch keeper with a thunderous strike from 15 yards.
The warning signs were there for a United side who constantly gave the ball away cheaply in midfield and Ribery finally restored parity with 76 minutes on the clock.
The manner of the goal was fortuitous in that his lacklustre 20-yard free-kick deflected off the advancing Rooney and left van der Sar flat-footed.
That brought United back to life and Nemanja Vidic rattled the crossbar with a crashing header from substitute Ryan Giggs' corner.
But with Rooney down in a heap in the centre circle after failing to stop Gomez, Bayern rubbed salt into the wounds in stoppage time.
The hulking Germany striker was allowed to run at goal and when Patrice Evra dallied on the ball in the box, it fell perfectly to Olic to pick his spot beyond van der Sar.
The goal was a bitter pill for United to swallow but all eyes will now be on Rooney and a probable injury lay-off with Saturday's Premier League title showdown with Chelsea next on the agenda.