The 22-year-old was criticised by manager Jose Mourinho for leaving the club's pre-season tour of the United States for the birth of his child and not returning stateside.
Martial has not reported back to the club since returning to Europe and does not feature against the Bundesliga champions at the Allianz Arena.
Nemanja Matic, Diogo Dalot, Sergio Romero and Antonio Valencia are missing through injury, while Romelu Lukaku and Jesse Lingard did not travel and Paul Pogba, Marouane Fellaini and Ashley Young are still on their post-World Cup breaks.
Bayern Munich: Neuer, Sule, Hummels, Thiago, Ribery, Martinez, Robben, Gnabry, Muller, Alaba, Kimmich
Subs: Ulreich, Lewandowski, Rafinha, Bernat, Boateng, Goretzka, Rudy, Coman, Mai, Zylla, Frantzke, Hoffman
Manchester United: De Gea, Darmian, Bailly, Lindelof, Shaw, Herrera, Fred, Andreas, Mata, Rashford, Sanchez
Subs: Grant, Fosu-Mensah, Jones, Mitchell, Smalling, Tuanzebe, Garner, McTominay, Chong, Greenwood
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