Goetze will have his ankle put in plaster for a week and will not return to training during an absence expected to last between 10 days and two weeks, the club said.
"The World Cup qualifiers will take place without him," Bayern said in a statement.
Schweinsteiger also dropped out of Germany's World Cup qualifiers against Austria and the Faroe Islands in September after failing to recover in time from an ankle injury suffered in midweek.
Schweinsteiger did not feature in Bayern's win on penalties over Chelsea in Prague on Friday.
The holding midfielder, who has 98 caps, picked up an ankle injury in Tuesday's 1-1 Bundesliga draw at Freiburg, but the knock was initially seen as not serious, with Germany coach Joachim Loew naming him in his squad on Friday.
Holding midfielder Javi Martinez and winger Arjen Robben were also nursing minor injuries and will miss training for a few days, Bayern said.
Germany host Austria in Munich on September 6 followed by the away tie against the Faroe Islands four days later.
(Reporting by Karolos Grohmann, editing by Stephen Wood)
