Winger Florian Thauvin continued his outstanding form with his 10th league goal of the season, with both players scoring in the second half.
Payet sent goalkeeper Remy Vercoutre the wrong way from the penalty spot in the 55th minute after Caen midfielder Vincent Bessat had clumsily fouled forward Bouna Sarr.
Thauvin all but sealed the result in the 74th, winning back the ball on the edge of the penalty area and then curling into the top left corner.
The 24-year-old Thauvin has scored several similar goals this season and is stating a strong claim to be included in France's World Cup later this year. The skillful and speedy winger has nine assists to add to his goals.
Payet, meanwhile, was at the heart of Marseille's best moves. Forward Clinton N'Jie header over his cross in a rare first-half attack from Marseille.
Marseille, which kept a third straight clean sheet, is two points ahead of third-place Lyon and four ahead of fourth-place Monaco. Caen, which was toothless in attack, is 10th.
With PSG streaking ahead at the top and scoring for fun, it looks increasingly like a three-way scrap for second spot.
Lyon is at home to PSG and Monaco hosts last-place Metz in Sunday's games.
Copyright 2018 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.