The forward and Adrien Rabiot were benched for the trip to the Velodrome by PSG boss Thomas Tuchel.
It was a big call from Tuchel as Mbappe has been bang in form after winning the World Cup, hitting 14 goals in 15 games for club and country.
Former Stoke City forward Eric Maxim Choupo-Moting replaced the 19-year-old striker in the Ligue 1 champions' starting line-up at the Velodrome.
Rabiot has also been a regular starter for Tuchel this term but his place was taken by German attacker Julian Draxler.
However, with the game goalless after an hour, Mbappe replaced Choupo-Moting and within three minutes opened the scoring.
Rabiot, whose contract is up at the end of the season and has been linked with a move away from the Ligue 1 giants, came on with 12 minutes remaining.
After the 2-0 win, Tuchel revealed why the pair were dropped.
He said: “Why didn’t Mbappe and Rabiot play? It’s a disciplinary situation. We had to, and we have to do that.
“You can think about as though it’s as if only one player comes late to one session, he is not out, but the collective is always more important than individuals, always.
“Mbappe gave the best answer when he came on to the field. We expect that from him.
“But I can tell you that I don’t like to deprive myself of Kylian.
“I hate to play without him in a match like that, but you have to make that decision.
“For me, personally, it was not a good evening – but I’m happy with those who were there and played.”
After 11 games, PSG have a commanding eight-point lead at the top of the table and can press home their dominance on Friday at home to their nearest rivals Lille.
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