"He strained his ankle," coach Pep Guardiola told reporters. "Tomorrow there will be a medical check. I hope he can play on Friday but we do not know that yet."
The Germany international, who had foot surgery in the close season and raced to be fit in time for the Bundesliga start, limped off in the 78th minute after going down unchallenged.
"It does not look good," said captain Philipp Lahm.
Champions League winners Bayern, who take on Europa League champions Chelsea, are already without their Spain midfielder Thiago Alcantara who had surgery on his right ankle this week.
Holding midfielder Javi Martinez is just returning to full fitness after an abdominal injury.
(Reporting by Karolos Grohmann; editing by Ken Ferris)
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