Corentin Tolisso struck twice as Bayern gained a measure of revenge for September's 3-0 defeat in Paris with a comfortable victory at the Allianz Arena on Tuesday in their final group game.
With both teams already through to the last 16, Bayern needed to win by four goals to usurp the French side from first place in the group.
Despite the defeat, the big-spending Parisians finished as Group B winners with a better goal difference across the two head-to-head matches.
However, the German champions restored pride as they matched PSG's tally of 15 points.
Bayern raced into a 2-0 half-time lead thanks to goals by Robert Lewandowski and Tolisso.
Kylian Mbappe calmed the visitors' nerves just after the break before Tolisso scored a superb third for Bayern.
PSG will go into the pot for Monday's draw as group winners, but Rabiot says they must improve following a second consecutive defeat after the Ligue 1 leaders lost 2-1 at Strasbourg last weekend.
"It's true that we have work to do because we need to play better in this type of match," said the defensive midfielder.
"We did some good things, but there's quite a lot we have to correct. We played too much as individuals and not enough as a team.
"When we played as a team, we were dangerous and could have scored more goals but weren't clinical enough.
"When we try to do everything on our own, it doesn't work."