The veteran goalkeeper and club captain needed treatment during a cooling break after reportedly making several circular movements with his arms in an attempt to loosen the affected shoulder.
Neuer was then treated on the ground, raising concerns over his fitness with Bayern preparing for their next Bundesliga fixture.
However, the initial signs were positive. The 40-year-old goalkeeper returned to training after receiving treatment and completed the session without any obvious problems.
That will come as a relief to Bayern, with Neuer set to continue as their first-choice goalkeeper for the new campaign. The club captain has also confirmed that the upcoming season is expected to be his last as a professional.
Bayern will now monitor Neuer's shoulder closely over the next few days to determine whether he can train without restrictions.
Their next Bundesliga match is against VfB Stuttgart at the Allianz Arena on Friday, with Bayern hoping Neuer's latest setback proves to be nothing more than a minor scare.