Thiago Alcantara, Gokhan Gonul's own goal and Sandro Wagner gave Bayern an 8-1 win on aggregate following the side's 5-0 victory in the first leg of the last-16 tie.
Lewandowski polished off the win with two late goals to give Bayern a seemingly insurmountable five-goal cushion ahead of the second leg of the last-16 tie in Istanbul on March 14.
Reus was handed the captain's armband 259 days after the German forward sustained a cruciate ligament injury in the German Cup final.
The German Clasico saw the league leaders Bayern Munich knockout arch-rivals Borussia Dortmund as Muller and Boateng shined in goal.
Bayern Munich, who have now won six straight matches since the return of Jupp Heynckes as coach, are guaranteed a top-two finish alongside Paris Saint-Germain.
PSG players still felt pretty motivated, especially following their 3-0 home victory over Bundesliga powerhouse Bayern Munich in the Champions League group match.
Ancelotti acknowledged he would face criticism for his lineup but remained defiant after the game against PSG in the Champions League.
Mbappe, who was hired alongside Neymar this summer, did not score but tormented the Bayern defence throughout with his dribbling ability and frenetic pace. He was decisive in setting up Neymar's goal.
Goals from Robert Lewandowski and Arjen Robben counted for little as Bayern dropped points for the second time in six games following a lacklustre performance.
While the Colombian midfielder made his first league start for Bayern, American teenager Weston McKennie did likewise for the home team.
Robert Lewandowski marked his 100th league appearance for Bayern with his 81st and 82nd goals, which came on the first day of the 184th beer festival.
Ancelotti, who has been irritated by questions over his rotation policy, faces added pressure after being outshone by Hoffenheim's coach Julian Nagelsmann.
Counterpart Carlo Ancelotti was left pondering how his side lost after 23 efforts at goal.
Europe giants such as Juventus, Chelsea and Manchester United were favourites to land the 20-year-old but it was Ancelotti that decided where the young colt would play and that is Swansea City.
Bayern Munich won the DFL Supercup against arch rivals Borussia Dortmund in the Signal Iduna Park in a penalty shootout with star man Robert Lewandowski stepping up.
The Gunners finally get a win over the Bavarians as they claim the International Champions Cup in a thriller of a match which was decided by a penalty shootout.
The Bavarians claim their fourth Telekom Cup after defeating Werder Bremen 2-0 to clinch the title as they keep adding the silverware to their tally. Rodriguez shines on his debut with an assist.
The Real Madrid attacker is now heading towards the German Champions Bayern Munich on loan as the player only made 22 appearances last season
The Chilean striker's future seems bleak as he still has a 1-year deal left with the Gunners and no decision has been made yet
Paris: Arsenal remains bottom of Group F in the Champions League but the Gunners finally got their campaign underway with a 2-0 win over Bayern Munich on Tuesday.After losing both opening matches for the first time,
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