Magalhaes and Fonte sealed an emphatic win for Lille with a header each in the 72nd and 84th minutes, respectively.
The French champions went on to concede four times in the second half for their heaviest league defeat under their Qatari owners.
PSG needs a win at Nantes on Wednesday to guarantee the league title, although a draw would likely be enough at the end of the season given PSG's huge advantage on goal difference.
PSG remain 17 points clear at the top of Ligue 1 and will be expected to wrap up the title against Nantes in midweek, but Lille enjoyed one night of swaggering dominance as they strengthened their grip on second place.More news: Finnish Social Democrat leader Rinne declares victory in election
The Parisiens thought they had taken an early lead when Mbappe touched home Meunier's cross, but the goal was correctly disallowed for offside, and moments later it was Lille who went ahead.
"You can lose, but you must lose in a certain manner - we cannot lack character like we did here", said the France worldwide.
Four minutes later, Bernat volleyed home from Mbappe's cross to equalise.
He told reporters: "It's too much, we miss so many players, it's not possible like that".
"It's not normal. We lack personality, it's one of our flaws, we have to correct this". "We made a good start to the match, with four goals, two for us and two offside".
Coach Thomas Tuchel did not share the player's point of view, pointing out that PSG only had 15 players available for the match.More news: Stacey Dooley breaks silence over Kevin Clifton scandal
"Today we played like amateurs".
"They didn't have any chance in the first half, and there was Kehrer's opportunity in the beginning of second half. To win here, we would have needed more quality".
"Yes, we're missing Lass Diarra and Adrien Rabiot".
"Nobody said anything before because we were winning".
Earlier, Saint-Etienne kept the pressure on Lyon and Marseille in the race for third spot with a 3-0 home win against Bordeaux.More news: Cavs Draw No. 2 Seed in Critical Lottery Tiebreaker