Thomas Mueller grabbed a 13th-minute opener at the Allianz Arena before fellow Germany worldwide Joshua Kimmich netted his seventh goal in all competitions this season.
Ancelotti had threatened changes for the Eindhoven match and admitted his team s attitude in Frankfurt was poor.
This season, they haven't performed to the same level under Carlo Ancelotti, with the drop in standards finally showing in the last four encounters as they scraped a late victory at lowly Hamburg were beaten by Atletico Madrid in Europe and held by Koln and Frankfurt in the league, yet there is nobody to capitalise and they remain two points clear of Koln and RB Leipzig at the top. But Bayern's defense showed some weaknesses when PSV stepped up the pace after its goal. "I feel good. All we are thinking about is three points".
"We started very well, dominated straight away and put them under pressure", said the Dutchman as Mueller and Kimmich both netted in the first 21 minutes.
Nonetheless, Lewandowski's return will no doubt come as a massive boost for the German champions - the Poland worldwide has hammered in nine goals in 11 appearances in 2016/17. "The Champions League is up on Wednesday and we absolutely must take three points", said Lahm.
Earlier, another cross from Alaba hit Hector Moreno and bounced off the post.
19/10/16 Bayern Munich's goalkeeper Manuel Neuer receives a goal by PSV Eindhoven's Luciano Narsingh (not pictured). Gaston Pereiro sent a through ball for Narsingh, who unleashed a fierce shot.
Seemingly stung by those near-misses, Bayern mounted an immediate response and duly made it 3-1 just short of the hour.
And Aboubakar then nodded in his second goal of the game from Ricardo Quaresma's free-kick late on, ensuring Napoli dropped points for the first time in this year's competition as Group B was blown wide open.
The UEFA Champions League's so-called "Group of Death" resumes play Wednesday with a clash between German and Dutch soccer powers.
The German World Cup victor and FC Bayern legend, Paul Breitner, will select 10 best players from the top eight teams who make it for the nationals finals, and these 10 players will represent the country in the FC Bayern Youth Cup World Finals in Munich in May next year.