"Besiktas were undefeated at home so far and to not be that focused after a 5-0 win is human", he said.
Besiktas did have one back just before the hour when Vagner Love slotted into the bottom corner of the net.
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Wagner, who joined Bayern in the January transfer window, has already scored in the Champions League qualifying rounds for Hoffenheim this season as well as in the Europa League.
"In the second half we were not really in control".
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.
Bayern's 8-1 aggregate win over Besiktas sees the Bundesliga leaders - who can wrap up the league title at the weekend - march on.
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Nevertheless, Lewandowski played until the 67th minute, but failed to add to his 32 goals this season in all competitions.
Domestically, Besiktas have gone unbeaten over their last eight games, picking up 20 points to move to second place.
With 18 minutes gone, Bayern captain Thomas Mueller swung in a cross and the Spain global thumped the ball home from close range.
The German giants were firmly in control of the contest after Thiago Alcantara and an own goal from Gokhan Gonul put them 7-0 up on aggregate until weird scenes unfolded in the 49th minute.
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But that was as good as it got for the hosts and Wagner chested in Alaba's deflected cross six minutes before the end after Bayern found too much space down the right side of Besiktas' defence.