Lewandowski scored in the 30th and 44th minutes and set up Mario Goetze in the 75th. The 19-year-old Goetze returned the favor for the Poland striker to complete his hat trick in the 78th.
Bayern goalkeeper Manuel Neuer has now gone 1,018 minutes without conceding a goal, but the league leader was unable to build on its run of 10 wins in all competitions.
Bayer Leverkusen beat Wolfsburg 3-1, Nuremberg drew 3-3 with Mainz while Freiburg beat third place Borussia Moenchengladbach 1-0 for only its second win of the season.
Hertha Berlin hosted Cologne later Saturday.