The visitors started brightly but were reduced to 10 men early on when Domagoj Vida was shown red, allowing Muller and Lewandowski to profit in front of goal.
Relive how the 90 minutes of action unfolded with Sports Mole's live text coverage below.
STARTING XI: Ulreich; Hummels, Javi Martinez, Boateng, Alaba; James, Vidal, Kimmich; Muller, Lewandowski, Coman
SUBS: Starke, Wagner, Sule, Ribery, Robben, Rafinha, Tolisso
STARTING XI: Fabri; Adriano, Pepe, Vida, Erkin; Quaresma, Medel; Hutchinson, Talisca, Babel; Love
SUBS: Tolga, Tosic, Gokhan, Lens, Tolgay, Oguzhan, Negredo
Jupp Heynckes: "They won all three of their away matches in the group stage. They won't hide, they like to play attacking football - if you let them. Besiktas are packed with international experience. They're well organised defensively and know how to counter well, they will look for their chances. I have no A or B team. We only have one Bayern team. Every player knows their position and understands each other, so I don't think we have too many problems with rotation."
Senol Gunes: "Yes we are the winners from the group but we will play with an important and powerful team. The football to be played tomorrow is real. We will reflect this fact on the field. Bayern's staff can make a few changes, a team that will be successful in this game. We are a team with an understanding of offence but we will also hold the defence against Bayern and we will also try to score goals."
BAYERN MUNICH SUBS: Starke, Wagner, Sule, Ribery, Rafinha, Tolisso
BESIKTAS SUBS: Tolga, Tosic, Gokhan, Lens, Tolgay, Oguzhan, Negredo