The Germany international, who had foot surgery in the close season and raced to be fit in time for the Bundesliga start, limped off with a strained right ankle in the 78th minute at Freiburg after going down unchallenged.
"Bastian Schweinsteiger did not injure himself seriously in the 1-1 draw at Freiburg," the Munich club said after the player's medical checks on Wednesday.
"The medical examination showed he sustained a strained ankle. On Wednesday and Thursday he will be treated intensively so that ideally he can take part in the final pre-game training on Friday."
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.