The Argentine has scored three times for PSG in as many games in Europe, but had yet to open his account in the French top flight after five appearances.
"I've had several chances, in this match and in previous matches," he said.
"I'm very happy with this first goal in Ligue 1 even if I had already scored in the Champions League."
Mauricio Pochettino's side increased their lead at the top of the table to 12 points over Rennes, who moved into second place with a 2-0 victory over Montpellier.
Messi missed PSG's past two games before the international break through injury, but returned to form a fearsome attack alongside Neymar and Mbappe after leading Argentina to a place at the 2022 World Cup.
Nantes had beaten PSG on their last visit to the capital in March, but Mbappe ensured the hosts made an ideal start by redirecting Leandro Paredes' long-range effort past Alban Lafont.
The France star has scored seven times in his last four outings after netting five goals for his country in World Cup qualifying wins over Kazakhstan and Finland over the past week.
Lafont produced a series of fine saves to keep Nantes in the game, twice thwarting Messi while also denying Neymar and Mbappe with his legs.
NAVAS RED CARD
Nantes sensed their opportunity though when Navas was shown a red card on 65 minutes for flattening Ludovic Blas after charging outside his area in pursuit of a long ball.
With Gianluigi Donnarumma ill, third-choice Sergio Rico came on for his first appearance of the season at Neymar's expense, almost immediately making a brilliant reflex stop from point-blank range.
Rico again reacted sharply to repel a header from Kolo Muani, but the Nantes striker was quickest to the rebound and back-heeled over the line -- with goal-line technology confirming the ball had crossed before Rico parried clear.
PSG regained the lead through a huge stroke of luck as Appiah's attempt to cut out a pass from Messi looped over a stranded Lafont from 20 metres.
The six-time Ballon d'Or winner then sealed the points four minutes from time, receiving a pass from Mbappe 35 metres out and drifting towards the area before sweeping into the far corner.
Later Saturday, Rennes continued their excellent run of form as a confident win over Montpellier extended their unbeaten run to 11 matches in all competitions.
Goals inside the first half-hour from Martin Terrier and Croatian international Lovro Majer saw them leapfrog Lens, Nice and Marseille into second place. (AFP)