The Germany international lasted half an hour against Mainz before having to be replaced but he is confident he will be back to face the league leaders next week
The 22-year-old was substituted in the 31st minute after a collision with Nikolce Noveski but although he is likely to miss Tuesday's clash with Dusseldorf, Gundogan is confident that he will be fit to face the league leaders next weekend.
"Noveski didn't mean to injure me, it was an unintentional result," Gundogan told Ruhr News. "At first I thought it would just be sore, but after getting back up and trying to run on it I realised that I would have to come off.
"We don't know the extent of the damage yet, but I hope that it isn't that bad. All we can do now is wait until we return to Dortmund."
Looking ahead to BVB's upcoming matches, Gundogan said: "Obviously, the match against Bayern Munich [next Saturday] is a highlight, a real showdown, but we must first focus on our game against Dusseldorf on Tuesday."
Dortmund, who face Dusseldorf in their upcoming match, currently lie second in the Bundesliga table, nine points behind the Bavarians.