Manuel Never played the full 90 minutes as Bayern were beaten 1-0 by rivals Borussia Dortmund on Saturday, but he will not travel to Russia.
The German goalkeeper was ruled out on Monday with the calf problem, meaning understudy Sven Ulreich and Tom Starke will compete for a starting place in the Group D.
Ulreich is likely to get the nod ahead of his 35-year-old team-mate after spending most of the campaign on the bench – the 28-year-old set for only his second Champions League outing for the club.
Bayern sit second in the group with two games to play but they, and Atletico Madrid, have already sealed progression to the last 16.
A 2-1 win over PSV last time out was enough to seal a top-two place.