The 20-year-old picked up the injury after coming off the bench in Germany's 4-4 draw with Sweden in Berlin on Tuesday in a FIFA World Cup™ qualifier, and will sit out the Bundesliga game with deep bruising.
"He has a problem with his thigh," said Dortmund coach Jurgen Klopp. "The problem was getting better, then he played 25 minutes and wrote me a text from Berlin saying: 'My hamstring has packed up'."
Question marks still hang over defender Marcel Schmelzer, who has a foot injury, while Ilkay Gundogan is nursing a back injury, but defender Mats Hummels and midfielder Sven Bender are both fit again.
"I am not sure yet who will play, but we will field a team which will demand everything of our opponents," added Klopp.
Klopp is hoping Gotze will be fit when Dortmund host Real Madrid in their third UEFA Champions League game of the season at Signal Iduna Park on Wednesday.