The Nerazzurri midfielder was in the starting XI at the Ernst-Happel-Stadion in Vienna, but his appearance did not last long.
The score was already at 1-1 by this stage in the Nations League clash.
Brozovic pulled up suddenly after making a pass and limped off clutching the back of his left thigh.
The player was suspended for the upcoming Serie A match against Roma anyway, so would not have been available next weekend.
However, if it is a thigh or hamstring strain, Brozovic could be out of action for several weeks.
The biggest concern is the Champions League head-to-head against Barcelona that is scheduled for October 4 at San Siro.
These teams will meet again at Camp Nou on October 12.
Bayern Munich are top of the group on six points, followed by Barcelona and Inter on three.