The starlet was dropped to the bench alongside team-mate Adrien Rabiot after the pair arrived late to the game.
However, Mbappe would have the last laugh as he stamped his mark on the derby less than three minutes after being introduced.
Eric Maxim Choupo-Moting made way for the World Cup winner with 62 minutes gone and by the time the clock had ticked around to 65 the visitors were ahead.
Marseille surrendered possession deep in the PSG half and the counter was swift and ruthless.
Angel Di Maria set Mbappe racing away with only Boubacar Kamara for company and the forward duly showed his blistering pace to burst past the 18-year-old and slide an effort beyond Steve Mandanda and into the far corner to break the deadlock.
The goal was Mbappe's tenth in Ligue 1 so far this campaign, making him the top goalscorer in Europe's top five leagues.