Marco Reus and Lukasz Piszczek have not recovered from injury in time to face Bayer Leverkusen on Sunday.
The last 16 of the Champions League sees three ties between Premier League and Bundesliga clubs, including Liverpool v Bayern Munich.
Werder Bremen captain Max Kruse scored the decisive penalty to book a place in the DFB-Pokal last eight at Borussia Dortmund's expense.
Bundesliga club Bayer Leverkusen mocked the low-scoring Super Bowl LIII on Twitter.
Bayern Munich would have had no trouble seeing off Bayer Leverkusen had Robert Lewandowski's goal been allowed to stand, said Niko Kovac.
Bayer Leverkusen star Leon Bailey felt he out-thought Bayern Munich goalkeeper Sven Ulreich with his brilliant free-kick on Saturday.
Bayern Munich led through Leon Goretzka, but second-half goals from Leon Bailey, Kevin Volland and Lucas Alario gave Bayer Leverkusen a win.
Sven Ulreich is in line to make his first appearance of the Bundesliga season after Manuel Neuer hurt his hand in Bayern Munich training.
Nico Kovac says Bayern Munich's pursuit of Callum Hudson-Odoi is over after confirming they will make no further signings this season.
Peter Bosz will take charge of Bundesliga club Bayer Leverkusen from January 4, replacing Heiko Herrlich.