Franck Ribery scored twice to take his tally to three goals in his last two Champions League games as the European champions sent out another message of intent.
Pep Guardiola's side dominated from start to finish, with David Alaba, Bastian Schweinsteiger and Mario Gotze also on target as Czech champions Plzen were totally outclassed.
Ribery (ankle) was passed fit to return to Bayern's starting line-up as Thomas Muller dropped to the bench.
The Germans wasted no time in putting the Czech champions on the back foot and Arjen Robben should have scored just five minutes in, when Mario Mandzukic nodded the ball into the Dutch winger's path, but he failed to hit the target from six yards out.
Kozacik then kept out a Van Buyten header from close range, but he could do nothing to prevent Alaba doubling Bayern's lead eight minutes before half-time when the Austrian full-back cut inside and found the bottom corner.
Plzen looked mesmerised by Bayern's slick movement and another fine spell resulted in Ribery crossing for Mandzukic to slot home from close range, but the striker was adjudged to be offside.
Three minutes later, Gotze made an instant impact after coming off the bench as he laid on a fourth goal for Schweinsteiger, who turned sharply and produced a clinical finish.
Gotze then got his name on the scoresheet in time added on when he converted Robben's inviting cross to seal the win.
