With Bayern already safe and assured of a spot in the round of 16, manager Vincent Kompany changed his side in several places, handing Jonas Urbig, Lennart Karl, and Nicolas Jackson starts ahead of Manuel Neuer, in-form Michael Olise, and Harry Kane.
PSV had all to play for in Eindhoven, with a win securing them a ticket for the knockouts and a draw needing results elsewhere to fall in their favour. Manager Peter Bosz's side was given a boost with the timely return of Guus Til, who missed last weekend's clash with NAC through injury and started as PSV's striker against the German giants.
After Tom Bischof hit the crossbar early from a free-kick, PSV had a bright start and tested Bayern goalkeeper Jonas Urbig early, especially via Joey Veerman, whose surprising shot from distance was kept out of the top corner by the youngster.
The two sides combined for a small dozen minor chances in the rest of the first half, with PSV's Guus Til and Ivan Perisic coming closest shortly before half-time, but neither found the net as PSV and Bayern headed into the break with a goalless draw on the scoreboard.
After PSV created chances but failed to place a shot on target, Bayern ruthlessly took the lead after ten minutes via Jamal Musiala, who emphatically fired the ball past Matej Kovar at the Czech's near post.
A cagey second half saw neither team find many breakthroughs, mostly thanks to Bayern's disciplined defending.
Even the Bavarian fortress couldn't stop Ismael Saibari, however, when the Moroccan starlet fired a rocket into Urbig's far corner to level the score and virtually put PSV in the knockouts with roughly 15 minutes remaining.
Harry Kane, who started on the bench in the UEFA Champions League for the first time since joining Bayern, restored the visitors' lead in the 84th minute, calmly firing the ball past Kovar to virtually eliminate PSV from the UEFA Champions League again.
The hosts failed to create a single chance following Kane's goal, leaving PSV hopeless in their fight for a spot in the knockouts. Former Europa Cup I winners were eliminated from the UEFA Champions League, finishing in 28th place with eight points.
Bayern Munich, meanwhile, secured their second-place finish with the win in Eindhoven and will return to the competition in the round of 16, which will take place between March 10 and 18.
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