The German record champions were handed a disappointing defeat at the BayArena as the 28-year-old's goal put the hosts in control, while the former Braunschweig man settled it late
In spite of a good start from the visitors, the brilliant Bernd Leno kept a clean sheet for Leverkusen, and late goals from Stefan Kiessling and substitute Karim Bellarabi were enough for Robin Dutt's side to claim three points.
Bayern nearly stormed into the lead after three minutes when David Alaba's diving header was saved superbly by Bernd Leno, while Toni Kroos could only fire the rebound wide.
The visitors continued to dominate possession as the half wore on, but were finding it difficult to create any clear cut opportunities against an organized Leverkusen outfit.
At the other end of the pitch, the hosts posed an intermittent threat on the counter, and twice went close as the match neared the half hour mark.
Stefan Kiessling first saw a one-on-one parried brilliantly by Manuel Neuer, before playing in Andre Schurrle for a weak volley that the Bayern keeper smothered with relative ease.
Emotions were running high on the pitch, with Rafinha forced to step between Thomas Muller and Jerome Boateng as the pair furiously remonstrated with one another following a missed assignment.
However, despite the flare up, Bayern continued to look the stronger side and with Arjen Robben at the heart of things, got ever closer to breaking the deadlock.
The Dutch winger, drafted onto the left flank due to the absence of Franck Ribery, sent in a glorious cross that Thomas Muller headed agonizingly wide, before slipping in Mario Gomez who rounded Leno, but saw his finish hacked away from goal by Manuel Friedrich.
With only a few minutes to go until half time, Neuer was forced to race off his line to expertly deny Schurrle, who had broken free of the Bayern defense to have a clear sight on goal.
The Bavarians dictated proceedings after the break, with Robben drawing a smart stop from Leno after breaking free down the left as the match neared the hour mark.
That was the cue for Leverkusen to come out of its shell, and a swift counterattack lead by Michal Kadlec saw Kiessling cushion a header into the path of Stefan Reinartz, who fired over the bar from yards out.
Kiessling then tested Neuer with a volley from point-blank range that the Bayern keeper did brilliantly to get his hands to.
Leverkusen was rewarded for its improved play with the opener in the 79th minute, after an acrobatic cross by Eren Derdiyok found Kiessling in close, who made no mistake to put his side into the lead.
Bayern continued to pour resources into attack, and were caught out on the counter attack in the 90th minute, when Gonzalo Castro stormed up the right flank before squaring to Bellarabi, who finished from close range.
The result means that Bayern could slip to third by late Sunday, depending on the result of Monchengladbach's game away to Nurnberg. Leverkusen, meanwhile, climbs to within four points of Schalke and a Champions League spot.