Khedira suffers knee injury
Khedira, who won his second cap against Argentina this month, had to be helped off after a clash with Bayern striker Miroslav Klose on the half hour.
"After treating him and an attempt to return to the pitch it was clear he could not go on," said Stuttgart in a statement.
"The midfielder will undergo further tests on Sunday and then we will be able to have a precise diagnosis."
The 22-year-old Khedira, whose form has been key in Stuttgart's rise up the table to seventh after a poor start to the season, is chasing a place in Germany's squad for the World Cup in South Africa in June.