Rooney was lying injured in his own half as Bayern broke forward on their decisive attack.
Ivica Olic applied the cool finish for Bayern's winner after Patrice Evra's lapse just inside the box.
At that moment United medical staff ran to Rooney, who appeared to land awkwardly on his right ankle after trying to avoid having his left foot trodden on by Mario Gomez. Rooney had earlier scored his 34th goal of the season before inadvertently deflecting Franck Ribery's free-kick past Edwin van der Sar 13 minutes from time.
Any enforced lay-off for Rooney at this stage of the season will be bad news in particular for Manchester United manager Sir Alex Ferguson but also for England.
Yet the night had started brightly for the England striker who met his boss's demand for an away goal after just 64 seconds.
Martin Demichelis chopped down Nani and his free-kick from the right flank looped skywards off Mark van Bommel for Rooney to volley home with his left foot.
Ribery was the architect of Bayern's fightback and but for van der Sar's fine goalkeeping, Bayern would have been level before the Frenchman's poorly-struck free-kick diverted off Rooney.
The free-kick had been given away by right back Gary Neville, and it was left-back Evra whose error led to Bayern's dramatic late winner which carried echoes of United's 1999 Champions League final win with a stoppage-time effort from Ole Gunnar Solskjaer.
To add to United's worries, they face Chelsea on Saturday in a vital Premier League encounter.