This was Mbappe's 21st Ligue 1 goal of the season and his 33rd in all competitions in 39 games.
PSG said Neymar is back in training, but coach Mauricio Pochettino does not want to take any risks with the Brazil striker, who has been sidelined for more than a month because of the injury.
Alessandro Florenzi scored PSG's second on 77 minutes and Pablo Sarabia notched a fourth for the reigning champions as PSG climbed above Rennes on goal difference after a fifth successive win.
Paris Saint-Germain were missing star striker Kylian Mbappé, who is recovering from ankle ligament damage sustained playing against Saint-Étienne, and now has other injury worries.
Kylian Mbappe scored a hat-trick as Paris St Germain thrashed 10-man Olympique Lyonnais 5-1 on Wednesday to reach the French Cup final and remain on course for a domestic treble.
French Cup: Pablo Sarabia nets brace as Paris Saint-Germain complete thumping win over Dijon to seal semi-final spot
Paris Saint-Germain’s Pablo Sarabia scored twice as they swept past Dijon and into the semi-finals of the French Cup with a 6-1 thrashing on Wednesday.
Ligue 1: Kylian Mbappe bags brace as Paris Saint-Germain ease past Monaco; Rennes stake claim to Champions League qualification
The sides drew 3-3 in Paris on Sunday night in arguably the season's most entertaining game, although this time Paris Saint-Germain kept Monaco's attack quiet and exposed one of the worst defences in the league
Coupe de France: Edinson Cavani, Pablo Sarabia bag brace apiece as Paris Saint-Germain thump six past amateur side Linas-Montlhéry
Paris Saint-Germain rested a number of star players but progression to the last 32 was never in doubt against a side which plays in the country's sixth tier
Ligue 1: Mauro Icardi nets first league goal as PSG thump Angers; Montpellier beats Monaco to climb to sixth place
Sarabia scored one goal and set up two more with Neymar completing the rout late as PSG kept a two-point lead over Nantes, which beat Nice 1-0 with an 86th-minute goal by Moses Simon. Angers is in third place, five points behind PSG.
Mauro Icardi scored his first Paris Saint-Germain goal as the French champions beat Galatasaray 1-0 to move four points clear at the top of their Champions League group on Tuesday.
Ligue 1: Paris Saint-Germain sign France U-21 defender Abdou Diallo from Borussia Dortmund on five-year contract
Abdou Diallo is PSG's fifth summer signing, with Spanish duo Pablo Sarabia and Ander Herrera having joined from Sevilla and Manchester United respectively.
Ligue 1: Paris Saint-Germain begin summer recruitment by signing Pablo Sarabia from Sevilla on five-year deal
Pablo Sarabia's arrival makes up for the departure to Bayer Leverkusen of teenage winger Moussa Diaby last month as PSG attempt to balance the books to avoid Financial Fair-Play sanctions from UEFA
LaLiga: Roque Mesa and Pablo Sarabia lift Sevilla back into European contention with win over Alaves
Goals from Roque Mesa and Pablo Sarabia lifted Sevilla back into European contention on Thursday with a crucial 2-0 win over Alaves.
Pablo Sarabia, Wissam Ben Yedder on target as Sevilla march to 2-0 win over Messi-less Barcelona in first leg quarter-final of Copa del Rey
Lionel Messi was rested and Luis Suarez left on the bench as Kevin-Prince Boateng made his debut for Barca in a match that Sevilla might even have been disappointed not to win by more.
La Liga: Wissam Ben Yedder's late goal rescues a point for Sevilla against Leganes; Valencia edge past Huesca
Mikel Vesga's header looked set to earn Leganes a valuable victory but Wissam Ben Yedder sneaked in to score in the 91st minute and earn Sevilla a 1-1 draw.
La Liga: Lionel Messi slams 31st league hat-trick to send Barcelona three points clear at top; Sevilla climb to second
Lionel Messi has scored five goals in two league games since finishing only fifth in the voting for the Ballon d'Or earlier this month.
Champions League: Bayern Munich ride on 1st leg victory to reach semis after goalless draw against 10-man Sevilla
Jupp Heynckes' Bayern Munich marched into another Champions League semi-final on Wednesday despite 10-man Sevilla holding them to a goalless draw at home in Wednesday's second leg.
Champions League: Bayern Munich gain advantage in quarter-final tie after narrow win at Sevilla in first leg
Bayern Munich placed one foot in the last four of the Champions League as Thiago Alcantara's header gave them a 2-1 win away to Sevilla on Tuesday in the first leg of their quarter-final in Spain.
Champions League: David de Gea's heroics help Manchester United hold Sevilla; Shakhtar Donetsk edge AS Roma
David de Gea deflected the attention away from Paul Pogba with another spectacular display of goalkeeping as Manchester United came away from their Champions League last 16, first leg against Sevilla in Spain with a 0-0 draw on Wednesday.
Champions League: Jose Mourinho needs to solve selection jigsaw for Manchester United's crucial trip to Sevilla
Jose Mourinho needs to figure out what is the best way to play all his attacking options if Manchester United wish to make a deep run in the Champions