Bayern are guaranteed a place in the top two in Group D following Tuesday's result in Eindhoven.
With two games still to play, Bayern are guaranteed a place in the top two in Group D following Tuesday's result in Eindhoven.
Poland hot-shot Lewandowski could have scored five goals, having also hit the woodwork on three occasions.
Having lost 4-1 away in Munich a fortnight ago, PSV took a shock lead when Santiago Arias headed the hosts ahead inside the opening quarter of an hour.
But Lewandowski converted a first-half penalty, then claimed the winner 16 minutes from time to dig Bayern out of trouble.
"It was not a good game from us today," fumed Bayern's Robben, who was making his first return to Eindhoven in a European game, 14 years after making his Champions League debut for PSV.
"It is just as well that we have qualified, but if we play like that in last 16, then we will have problems.
"We played without conviction, were much too slow.
"I looked for combinations with Thomas (Mueller) and Philipp (Lahm), but it was difficult.
"We must do better, we were missing something and we fail to impose ourselves."
With 25 minutes left, Bayern coach Carlo Ancelotti injected some pace by bringing on wingers Douglas Costa and Kingsley Coman for Robben and Joshua Kimmich.
It was not the return to Eindhoven Robben had wanted.
"Such a game is unique for me, of course you want to play 90 minutes, so I was disappointed and sad about the substitution, but the coach has his reasons," said Bayern's Dutchman.
Nevertheless, the switch paid off as Costa's superb pass split the Eindhoven defence to allow Alaba to get in behind to provide the superb pass for Lewandowski's winner.
"I tried to change the system to play with two wingers and open some space," explained Ancelotti.
"We did that and Lewandowksi scored.
"It was difficult at the start, but slowly we worked our way back into the game and got there in the end.
"We thought it was important to avoid counter attacks.
"We started to play quicker in the second half and create more opportunities.
"It was important that we didn't lose our confidence."
Dutch champions PSV's slim chances of qualifying are over with Phillip Cocu's side third in the section and eight points adrift of Bayern.
Bayern's home clash on December 6 against Atletico -- who are also through after beating Rostov 2-1 -- is likely to decide who wins the group.
"It was a painstaking start to the game, but we came back step by step and deserved the win," added Ancelotti.
"It was important that we did not lose our self-confidence after it went 1-1.
"We still have two games to reach first place.
"This is important, but qualifying was more important."