Thomas Muller opened the scoring with a penalty after home defender Marius Wolf had fouled Serge Gnabry.
Bayern doubled their lead when Gnabry curled a left-foot effort into the bottom corner before Dominick Drexler scored late on for the hosts.
Hansi Flick's side, who lead the table on goal difference, now have 15 points from their first six games.
Mats Hummels scored twice as second-placed Borussia Dortmund won at Arminia Bielefeld, while RB Leipzig are two points behind in third after losing at Borussia Monchengladbach on Saturday evening.
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