It came just six minutes after Messi had scored his first of the match, sweeping his finish into the bottom corner when set-up by the brilliant Neymar.
The Brazilian attacker had opened the scoring in an impressive performance before providing two more assists for Achraf Hakimi and Marquinhos to make it 3-0 before half time.
Messi then finished the night with a brace to give the reigning league champion an emphatic victory under new coach Christophe Galtier.
The result will be a warning shot to other teams in the French top flight given it came without starman Kylian Mbappe, who was absent through injury.
“The most important thing is to score goals, that is in Paris Saint-Germain’s DNA and the DNA of the players here,” Galtier told PSGTV after the game.
“So there is real satisfaction with those two elements of our game, attacking in numbers with lots of technical quality, and defending as a team.”