The Swiss forward, who replaced injured midfielder Javi Martinez in the opening half, struck in the 59th minute as Bayern failed to win for only the fourth time in their opening 17 games.
Torben Marx gave Gladbach the lead by converting a penalty harshly awarded for handball by Jerome Boateng.
The Bavarians reached the halfway point of the season with an impressive 42 points, 44 goals scored and just seven conceded.
Bayern are 12 points clear of second-placed Bayer Leverkusen who host Hamburg SV on Saturday. (Writing by Brian Homewood; editing by Tony Jimenez)
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