Mane was replaced by Leroy Sane in the 20th minute after appearing to indicate a problem around his right knee. He had earlier pulled up in apparent discomfort while sprinting to press an opponent.
After receiving attention from Bayern team staff on the pitch, Mane was able to leave the field under his own power and was seen applauding the home supporters as he made his way to the dressing room.
Bayern went on to win the match 6-1 with Serge Gnabry netting a hat trick to extend their lead in the Bundesliga to four points over Freiburg.
Bayern coach Julian Nagelsmann said after the match that Mane had taken a knock to the top of his shinbone and would have an X-ray to determine the extent of the injury.
"I can't say anything for sure, he took a blow to the head of his shin. That's an unpleasant spot, it radiates a bit into the muscles," Nagelsmann said.
"I think he has to go to the X-ray to see if there is something there, because it is splintering easily. But I hope that nothing is wrong. I can't say anything for sure yet."