Santiago Arias had stunned them early on, despite clearly being offside, however an equally contentious penalty award for Bayern gave Lewandowski the chance he needed to equalise.
He then scored in the second half, and was denied a brilliant third by the post, as Bayern safely saw their way to another three points to guarantee Champions League football in the spring.
Bayern looking to qualify whilst PSV battle injuries
In the reverse game two weeks ago, Bayern came out comfortably on top with a 4-1 victory, and went into this game with the knowledge that a win, combined with FC Rostov failing to win against Atlético Madrid, would see them through. PSV had to avoid defeat to avoid being eliminated.
Daniel Schwaab, formerly of SC Freiburg, Bayer Leverkusen and VfB Stuttgart, came in for Steven Bergwijn in PSV’s only change from their weekend win over Vitesse Arnhem. They are in the midst of an injury crisis however, with goalkeeper Jeroen Zoet, Siem De Jong, and Luciano Narsingh, the scorer in Munich, amongst those out.
After back-to-back victory in the cup and league against FC Augsburg, Bayern made three changes to their side. Mats Hummels, Joshua Kimmich and Thomas Müller came back in for Javi Martínez, Thiago, both of whom are injured, and Douglas Costa.
Offside goal cancelled out by harsh penalty
Bayern were threatening from the outset, with Müller shooting wide with Remko Pasveer looking beaten, before Lewandowski headed a Jérôme Boateng long ball into the bar and then headed over.
It was PSV who took the early advantage however, albeit in controversial circumstances. On the counter, Bart Ramselaar had his cross headed on by Arias to Davy Pröpper. Manuel Neuer saved but Arias, who was offside when Pröpper made contact, headed in the rebound himself. Neuer was, rightly, convinced it shouldn’t stand, but it did.
After a quiet phase of the game Bayern stepped it up. Arjen Robben, back at his former club, had a header diverted wide by Pasveer, before more controversy. Lewandowski headed the corner onto the post, but had Héctor Moreno all over him. No penalty for Bayern.
But then they did get one, in more dubious fashion. A Philipp Lahm cross off the boot from Kimmich went into the arm of Andrés Guardado, and despite him making no attempt to play the ball the referee pointed to the spot. Lewandowski made no mistake, sending Pasveer to wrong way to level the game.
Bayern had one chance to take the lead before half time. Müller crossed and Arturo Vidal struck, with Pasveer sticking out a hand and managing to keep a hold of the ball.
Lewandowski strikes again to send Bayern through
PSV threatened in patches early after half time, but they failed to create any chances, with an Arias blocked by Xavi Alonso, before Gastón Pereiro charged down the middle but was denied entry into the box by an excellent Hummels tackle.
Vidal had a great chance though to give Bayern the lead, only to be denied by an excellent save by Pasveer, before Moreno had to clear Müller’s rebound shot on the line.
Carlo Ancelotti introduced Costa and Kingsley Coman to add a bit of pace to Bayern’s attack, and it eventually came good. Costa combined with David Alaba, whose cross was turned in by Lewandowski.
He would almost score a superb third. Coman and Costa were involved again, with a world class, Dennis Bergkamp-esque flick past Schwaab from the Pole, only to hit the post, again, with his strike on goal.
But Lewandowski would not get that hat-trick, especially after Lahm forced him to concede a last minute free-kick to Alaba, but with Atlético beating Rostov 2-1 in the other game in Group D, Bayern book their place in the last 16 along with the Spaniards. The best PSV can hope for now is the UEFA Europa League.