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.
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.
PSG, however, controlled the game as Idrissa Gueye, back after being rested in Wednesday's 2-0 home loss to Amiens, and Marco Verratti, returning from suspension, stabilized the midfield.
PSG have now won all their six matches in all competitions without conceding a goal with Gueye on the pitch.
Earlier, Olympique Lyonnais's winless streak stretched to seven games in all competitions as they slumped to a 1-0 home defeat to Nantes.
Nantes prevailed thanks to a 58th-minute own goal by Fernando Marcal and the Canaries, with 16 points from eight games, are second in the standings.
Lyon, who travel to RB Leipzig in the Champions League on Wednesday, dropped to 11th on nine points.
The outcome of the game increased the pressure on coach Sylvinho, who replaced Bruno Genesio during the close season, after club president Jean-Michel Aulas said this week that he expected results.
"We will talk tonight. The president is not happy, obviously," said sports director Juninho, who was recruited alongside Sylvinho.
"We will see which decision he will make."