The pair were the latest additions to a growing injury list for coach Joachim Low, who needed to call up three replacement players after Friday's 3-0 win against the same opponents in Astana.
Howedes suffered his problem in Kazakhstan while Gomez was injured the day before last week's game. Both players were on their way back to their clubs for further medical treatment, Germany said in a statement.
Germany top Group C on 13 points from five games, with Sweden in second place on eight from four matches.
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