Sydney Lohmann opened the scoring 12 minutes in with a powerful header after Glas' right-footed cross bounded off the hands of Chelsea goalkeeper Ann-Katrin Berger. Melanie Leupolz tied it against her former team in the 23rd minute.
Glas carried the ball down the right before cutting inside and unleashing her decisive strike from the top of the box in the 56th minute.
"Hanna is one of the best right backs in the world," said Bayern coach Jens Scheuer, though adding he was "surprised that she can score with the left foot. I underestimated her a little bit."
Chelsea midfielder Ji So-yun's long-range attempt hit the crossbar in the 73rd minute.