Mbappé took a pass from striker Goncalo Ramos and masterfully played it back into his path as Ramos ran into the penalty area in the 85th minute of Saturday's match.
PSG are 13 points clear of second-placed Brest, who host relegation battlers Metz on Sunday, and a record-extending 12th league title seems a formality. After this weekend, there are only six rounds and 18 points remaining.
PSG face Barcelona in the first leg of their Champions League quarter-final at Parc des Princes on Wednesday, and coach Luis Enrique left out Mbappé, goalkeeper Gianluigi Donnarumma and other first-teamers. Mbappé went on against Clermont midway through the second half.
Enrique has been rotating Mbappé in recent weeks, even taking him out midway through the second half against bitter foes Marseille last Sunday.
Midfielder Senny Mayulu and defender Yoram Zague, who are both aged 17, started their first games for PSG.
But PSG gave away a sloppy goal in the 32nd when central defender Milan Skriniar failed to deal with a cross.
The ball was quickly played back into the penalty area, where Clermont defender Habib Keita hit a scuffed shot which bobbled past goalkeeper Arnau Tenas.
Mayulu scored with a fine shot deep into first half stoppage time, but the goal was ruled out after video picked up a blatant foul by Zague moments earlier.
Right back Achraf Hakimi hit the crossbar in the 63rd and Enrique sent on Mbappé moments later.
US forward Emmanuel Sabbi scored a late penalty after being fouled to earn struggling Le Havre a 1-1 draw at fifth-placed Lens.
Sabbi's fifth goal of the season moved Le Havre up one place to 14th.
Lens striker Elye Wahi looked sharp early on but Le Havre held firm until the 58th when Przemysław Frankowski's cross looped over goalkeeper Arthur Desmas.
Sabbi netted in the 78th after being pushed in the back when contesting a high ball.
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