The hosts were rampant from the off, weighing in with a number of chances before opening the scoring in the 13th minute through Thomas Muller, who forced Jeroen Zoet into a save following an inswinging corner but stabbed home on the rebound.
Towards the end of the first half, however, Phillip Cocu's charges enjoyed a bright spell as they saw a goal chalked off for offside before getting onto the scoresheet four minutes before the break through Luciano Narsingh's powerful shot off the post.
Both sides weighed in with dangerous chances early in the second half but Carlo Ancelotti's side went on to extend their lead just before the hour, Robert Lewandowski getting onto a goalmouth rebound and heading home.
Bayern finished off by adding gloss to the scoreline late on, as Thiago Alcantara's lofted cross into the box fell to Arjen Robben, who nodded the ball into the middle of the goal and beyond the goalkeeper.
The result means that the Bundesliga giants remain second in Group D, three points behind Atletico Madrid but five ahead of third-placed Rostov, while PSV sit fourth on one point.