The 29-year-old midfielder had to be taken off with eleven minutes remaining in Tuesday's 1-1 draw with Freiburg after picking up an ankle injury.
"He [Schweinsteiger] will be examined in Munich," explained Bayern's director of media Markus Hörwick. "We are hopeful he'll be able to play in Prague on Friday."
On Wednesday afternoon the club revealed that the damage was not as serious as first thought, using their official Twitter channel to say: "The injury sustained by our vice-captain against Freiburg is only a sprained ankle. He should be fit to train on Thursday."
The news comes just days after summer signing Thiago Alcantara was ruled out for at least seven weeks following ankle surgery.