Upamecano was left out of the starting line-up as Bayern coach Julian Nagelsmann reverted to a back three following a catastrophic defensive display in the 4-2 loss on Saturday.
The 23-year-old faced criticism for his performance against Bochum, with Bayern legend Lothar Matthaeus saying he looked "out of place" at a media event on Monday.
Bayern also lined up without goalkeeper Manuel Neuer, who is still recovering from knee surgery and misses out on a Champions League fixture for the first time this season.
Sven Ulreich replaced Neuer between the sticks, while veteran forward Thomas Mueller assumed the captain's armband.
Salzburg, meanwhile, were without Brazilian full-back Bernardo, who is also out after a knee operation.