- Besiktas have now lost all four of their Champions League matches against Bayern, losing by an aggregate score of 1-12.
Having resisted the urge to name a weakened team after their first-leg romp, Bayern wasted little time taking the lead against the Turkish champions.
But he lasted just 35 minutes before being substituted.
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Left unmarked at the back post, the Spain global raced onto a Thomas Müller cross from the right and coolly slotted home on the volley with his left foot from close range after just 18 minutes.
Nevertheless, Lewandowski played until the 67th minute, but failed to add to his 32 goals this season in all competitions.
Hummels, who along Jerome Boateng was booked in the first half, was replaced by Niklas Suele at the break before Bayern extended their lead thanks to a Besiktas own goal.
They did manage to pull a goal back through Vagner Love's effort in the 58th minute which breathed some brief life into the hosts and the 40,000 home fans.
Bayern extended their lead moments after the start of the second half when Turkey global Gonul flicked the ball into his own net from a Rafinha cross.