Germany international Schweinsteiger, who had returned to action only at the start of the year following shoulder surgery in November, will miss the club's Champions League last 16 first leg against FC Basel later this month.
It was not clear, however, how long Schweinsteiger, who hobbled off the pitch in Stuttgart after 17 minutes, would remain out of action.
"A forecast when he can return to training and when he can play again will be given at a later date," Bayern doctor Hans-Wilhelm Muller-Wohlfahrt told the club website.
He said the 27-year-old's leg had been put in a cast for a week and the player would then switch it for a special shoe.
Bayern are chasing an unprecedented German treble of domestic title, cup win and the Champions League.
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