As Mustafi attempted to win the ball back for Germany, he clutched his upper thigh and collapsed to floor.
To compound matters, Azerbaijan continued to play and scored an equalising goal in the first half.
Mustafi was then carried off by the Germany medical team and replaced by Matthias Ginter.
The defender is set to undergo scans but he is likely to be a major doubt for Arsenal’s next match against Watford on Saturday.
Arsenal already have defensive concerns with Laurent Koscielny struggling with an Achilles problem.
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The French defender missed Arsenal’s win against Brighton before the international break.
Per Mertesacker could make his Premier League appearance of season alongside Rob Holding and Nacho Monreal.