Gomez, the only striker left in the squad after Miroslav Klose was ruled out weeks ago with an injury, was hurt during the final training session late on Thursday evening, the German football association said.
"The 27-year-old will not be training for about two days," it said in a statement.
Germany coach Joachim Loew's dilemma whether to play without an out-and-out striker has accordingly been lifted with offensive midfielder Mario Goetze, favoured to start even before Gomez' injury, securing the starting spot.
Germany, who are top of the 2014 World Cup qualifying Group C with 10 points from four games with Sweden in second place on seven from three matches, next play Kazakhstan at home on March 26.
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- Miroslav Klose