The striker was set to line up for his national side in Dusseldorf on Wednesday, less than two months after Germany beat Argentina in the World Cup final.
However, the former Real Madrid man has been laid low by injury and will play no part.
Napoli will hope that Higuain's injury is not too severe as they prepare to cope with the additional demands of UEFA Europa League fixtures.
"Gonzalo Higuain suffered a muscle problem in training with [the national team]," read a statement on Napoli's official website.
"[He will] watch the match with his team-mates and then will return tomorrow to Naples where he will be visited by medical staff."
Higuain started Napoli's opening Serie A match on Sunday, a 2-1 victory at Genoa.
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