Mbappe, back as a substitute after a lengthy injury, burst down the right flank in the 70th minute and Neymar just had to tap in as PSG reclaimed the league lead with 18 points from eight games.
They lead Nantes, who snatched a 1-0 win at Olympique Lyonnais, by two points.
"I am happy. However, the most important thing is being able to help the team. That is why I am here -- at the team's disposal. It is what I was hoping to do and it is always good to score in an encounter as difficult and tight as this one," Neymar told BeIN Sport after the win.
PSG travel to Galatasaray in the Champions League on Tuesday, without the suspended Neymar, who has scored his team's last three goals in Ligue 1.
Mbappe, who missed a month of competition with a muscle problem, played only 30 minutes as a second-half substitute but his impact was immediate after a dull first half.
"I should have scored at least once or twice, but I am back in the swing of things. I set Neymar up and we are going home with all three points -- all is good," Mbappe told Canal+ afterwards.
"I tried to find Neymar, sometimes when I should not have done, but I also did not when I should have," Mbappe added. "However, we have a good understanding. I set him up today and he won it for us."
PSG coach Thomas Tuchel was coy on whether Mbappe will start against Galatasary, saying "everybody needs some rest."
"We dominated the match and created many chances -- it was one of our best away performances," Tuchel said. "My main grumble was that we only scored once, which was why it was so tight right up until the end."
Information from ESPN FC's Jonathan Johnson and Reuters was used in this report.