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Manuel Neuer made life very difficult for the home side in the 17th minute when he was shown a straight red card after making a run outside of the box and clumsily bringing down Jeremie Frimpong, who was chasing down a long ball.
With Sven Ulreich unavailable for personal reasons, Bayern's third-choice goalkeeper, Daniel Peretz, came on in Neuer's place.
Despite being reduced to 10 men, and with Harry Kane out injured, Bayern created a handful of opportunities.
Leverkusen coach Xabi Alonso introduced in-form striker Patrik Schick in place of Robert Andrich. Things didn't get any better for Bayer 04 when Schick injured in the 61st minute replaced by Nathan Tella. Just the man who broke the deadlock in the 69th minute, to give the visitors the lead.
Leverkusen held on until the final whistle to book their place in the quarter-finals and send Bayern out of the competition.
