The winger will be out of action for a number of days and will miss the Bavarians next match due to the knock, while Rafinha is doubtful after picking up an ankle problem
The versatile attacker was forced to bring a premature end to his training session on Monday after twisting his right ankle, and was diagnosed with a sprain by club doctor Hans-Wilhelm Muller-Wohlfahrt.
Shaqiri has been ordered to stay away from squad training for the next five days, and is therefore automatically ruled out of the league clash away to Mainz.
The 21-year-old has made 14 Bundesliga appearances for Bayern so far this term, netting once in the process.
Meanwhile, Brazilian defender Rafinha is doubt for the match against Mainz after picking up an ankle injury of his own.
The right-back has sprained his right ankle in training and will has been ordered to rest for the next three days.