Bayern entered Turkey with a commanding 5-0 advantage after a dominant performance against a 10-man Besiktas in Munich last month, and the excellent Thiago Alcantara wasted little time in adding a sixth on the day.
For Bayern coach Jupp Heynckes, who replaced Carlo Ancelotti in October, this was his 11th straight win in the Champions League which set a new competition record.
"Besiktas hadn't lost here in the Champions League, so it wasn't easy".
Besiktas is unbeaten since then, though, with three wins in league play and a 2-2 draw with Fenerbahce in the first leg of the Turkish Cup semifinal.
"It was a really hectic game", said Bayern captain Thomas Mueller.
Muller swung over a cross from the right and Thiago stole in at the far post ahead of Gonul to volley home first time with his weaker left foot.
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.
Just a minute into the second half, Bayern finally scored their second when Franck Ribery released overlapping full-back Rafinha and defender Necip Uysal lunged at the cross but missed and the backtracking Gonul diverted it past goalkeeper Zengin.
Yet Bayern substitute Sandro Wagner chested in a David Alaba cross with six minutes remaining to make sure of Bayern's victory.