Neymar, who signed from Barcelona in August for a world-record fee of €222million, may have been sidelined with a broken metatarsal since February, but 19 goals and 13 assists in 20 appearances earned him the honour.
The 26-year-old Brazil international succeeded team-mate Edinson Cavani and was presented with the prize by compatriot Ronaldo.
PSG completed a clean sweep of the domestic trophies for the third time in four years and Neymar will be desperate to make his comeback when the club draw their season to a close at Caen on Saturday.
The treble was not enough to keep Unai Emery at Parc des Princes next season as their Champions League struggles continued, but he was recognised as the Ligue 1 Coach of the Year.
Neymar was named in the Team of the Season alongside PSG team-mates Dani Alves, Marquinhos, Thiago Silva, Marco Verratti, Mbappe and Cavani. Marseille duo Mandada and Luiz Gustavo and Lyon pair Ferland Mendy and Nabil Fekir made up the XI.
Chelsea midfielder N'Golo Kante was named the Best French Player Playing Abroad.