Bayern steer clear of German Cup trouble
Thomas Muller won both penalties, which were converted by Mario Gomez and Bastian Schweinsteiger, to give new coach Jupp Heynckes a winning start to his third stint in charge of the Bavarians.
Muller himself added the third seven minutes from time for the 15-times German Cup winners in front of a crowd of 23,500 at Braunschweig, newly promoted from the third division.
Four Bundesliga clubs fell to lower league teams over the course of the weekend's first round ties.
VfL Wolfsburg lost at fourth division RB Leipzig while Werder Bremen and Freiburg lost to third division opponents and Bayer Leverkusen, last season's Bundesliga runners-up, squandered a 3-0 lead in a 4-3 extra-time defeat at second division Dynamo Dresden.