Messi, who started as a starter after being suspended by the club for lack of training last month, was booed by fans before and during the one-sided game.
Saint-Germain took their tally to 81 points, three games from the end, thanks to goals from Fabian Ruiz and Ashraf Hakimi, and a double from Kylian Mbappe, while Mohamed Youssef accidentally scored into his own net.
Coach Christophe Galtier’s side are six points ahead of second-placed Lens and 11 points over third-placed Olympique de Marseille, who host last-place club Angers on Sunday.
Ajaccio have 18 points from 23 games, 11 points ahead of 16th-placed Auxerre, and the bottom four teams, out of a total of 20 teams, are relegated to the second division.
Each team finished the game with ten players after Hakimi and Thomas Mangani were sent off late.
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