Alphonso Davies will miss 6-8 weeks due to ligament damage in his ankle.
Davies suffered the injury three minutes into Bayern's 5-0 win against Eintracht.
"He sustained a ligament injury. One ligament is fully torn, another is partially torn. We reckon he'll be sidelined for six to eight weeks. It hurts when a player of this quality is ruled out," said Hansi Flick.
Davies was replaced by Lucas Hernandez.