Neymar opened the scoring for PSG in Clermont before setting up Achraf Hakimi and Marquinhos for further goals before half-time.
Messi then exchanged passes with Neymar before sidefooting in the visitors’ fourth goal with 10 minutes left.
Yet Messi saved the best for last, darting into the box four minutes from the end to control a Leandro Paredes pass on his chest with his back to goal, before converting with an acrobatic overhead kick.
That goal had the crowd at Clermont’s Stade Gabriel-Montpied singing the name of the seven-time Ballon d’Or winner, who endured a difficult first season in Paris.
PSG’s victory in new coach Christophe Galtier’s first league game at the helm was achieved without Kylian Mbappe, who was absent due to an adductor injury.
Mbappe also missed last week’s 4-0 defeat of Nantes in the season-opening Champions Trophy due to suspension.
Messi had opened the scoring in that game, while Neymar netted a brace.