The Bundesliga champions were virtually through the next round even before a ball was kicked in Turkey after claiming a 5-0 win at home in the first leg.
David Alaba almost opened the scoring for the Bavarians this week in the 11th minute with a free-kick that was parried away by Besiktas shot-stopper Tolga Zengin, while Thomas Muller could not turn home the rebound.
However, Thiago Alcantara got the breakthrough in the 18th minute for Jupp Heynckes’s charges with a wonderful strike at the back post following a delicate chip by Muller.
The Turkish side were breaking out in attack on the right wing through Gökhan Gonul, but they could not find the decisive pass in the final third.
Robert Lewandowski had a chance to double the lead for the Bavarians in the 36th minute after being sent through by Arturo Vidal but he failed to find the target.
Nevertheless, the Bavarians took the 1-0 lead into the halftime break.
Gonul who had been impressive in the first half was unlucky to score an own goal a minute into the second stanza after he deflected Rafinha’s low cross into his own net.
Gonul redeemed himself on the hour-mark after dispossessing Alaba inside the box before picking out Vágner Love, who managed to poke home from close range to reduce the deficit.
However, Sandro Wagner bagged Bayern's third of the night six minutes before time after controlling Alaba’s cross at the far post before firing home at the far post to seal a 3-1 win on the night and 8-1 on aggregate.