The Ligue 1 champions lost 3-1 at Stade Auguste-Delaune to their eighth-placed hosts, but they were still able to make their mark thanks to Mbappe's scrappy 59th-minute effort.
The goal meant that PSG had become the first team to score in each of their 38 matches in France's top flight.
Mbappe's strike saw the World Cup winner comfortably end the 2018-19 campaign as Ligue 1’s top scorer.
His tally of 33 goals was not enough to catch Lionel Messi’s total of 36 in the race for the European Golden Shoe – a title the Argentinian held on to for a record third successive season.
However, the 20-year-old’s impressive haul was enough to earn him the honour of the top flight’s leading scorer for the first time in his career.
Sampdoria forward Fabio Quagliarella is currently third in the Golden Shoe list with 26, but would need a miracle in front of goal to trouble the top two of Messi and Mbappe when his side end their season against Juventus on Sunday.
Thomas Tuchel’s side achieved the accolade despite something of a late-season wobble.
Despite winning the division with 91 points – some 16 points clear of runners-up Lille, PSG managed to win just three of their last nine top-flight fixtures.
— OptaJean (@OptaJean) May 24, 2019
Mbappe sent shockwaves around European football earlier this week when he openly admitted he had reached a “turning point” in his career, suggesting his future may lie away from the French capital.
Speaking after accepting the Ligue 1 Player of the Year Award, the young striker claimed he would like a bigger role going forward.
That role, he said, could come either at PSG or “maybe somewhere else”.