The German Football Federation says Schmelzer had a recurrence of a metatarsal injury in his right foot. The same injury forced the Borussia Dortmund player out of Germany's 4-4 draw with Sweden in a World Cup qualifier last month.
Boateng is out because of a left groin injury sustained in Bayern Munich's 2-0 win over Eintracht Frankfurt on Saturday.
Bayern coach Jupp Heynckes confirmed Sunday that Boateng tore a muscle and that the 24-year-old player "will definitely be out for two or three weeks."
Boateng has played 28 times for Germany, while Schmelzer has nine caps.
Germany coach Joachim Loew did not immediately call up any replacements.
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