Peter Bosz's attack-minded Leverkusen scored three goals in the second half as Leon Bailey and Kevin Volland overturned Bayern's lead, from Leon Goretzka's 41st-minute goal, while Lucas Alario sealed the win with a late strike.
Bayern dropped to third place on 42 after Borussia Moenchengladbach moved into second place on goal difference following their 2-0 win at Schalke 04. Leaders Dortmund are on 49 after a 1-1 draw with Eintracht Frankfurt,
The defeat comes as Bayern prepare for a few busy weeks in all competitions, with the German Cup encounter at Hertha Berlin next week and their Champions League Round of 16, two-legged tie with Premier League leaders Liverpool later this month.
"The result does not really reflect the game," Bayern coach Niko Kovac told reporters. "We played a good first half. We should have scored a second early on as well.
"We knew Leverkusen would step on the gas in the second half and we wanted to be very compact. We did not fully succeed in that." Germany international Goretzka headed in a Thomas Mueller cross to put Bayern ahead with his fourth goal in the last three league games.
With Kingsley Coman wreaking havoc down the left wing it looked only a matter of time until the champions scored again.
But Bailey fired home a stunning 25-metre free kick eight minutes after the restart to level and Volland completed a stunning break that caught Bayern's defence napping to secure the lead.
Julian Brandt could have added another goal for the hosts a little later but Bayern keeper Sven Ulreich tipped his volley round the post.
Brandt then set up substitute Alario in the 87th for their third goal with a simple tap-in after another break.
(Reporting by Karolos Grohmann; Editing by Ken Ferris and Clare Fallon)
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