He turned his right ankle in the build-up to Bayern's late winner in the Champions League, limping off the pitch and leaving the stadium on crutches.
Rooney, 24, is set for a scan and is a doubt for Saturday's crunch Premier League game with title rivals Chelsea.
United boss Sir Alex Ferguson indicated the injury was "not terribly serious".
However, Rooney's situation will be a concern for
"He has obviously hurt his ankle," added
Rooney has been in scintillating form this season, scoring 34 goals in all competitions, and is regarded as being key to
It was an eventful night for the striker, who opened the scoring for United with a close-range volley after only 66 seconds before deflecting in Franck Ribery's free-kick for Bayern's equaliser.
And in the dying moments of the game, Rooney then appeared to be in severe pain after landing awkwardly on his right ankle after trying to avoid having his left foot trodden on by Bayern's Mario Gomez.
He left the ground on crutches and with his foot in a protective cast.