The result lifted Marseille up to seventh in the table with 24 points from 16 games.
Caen stayed 10th on 19 points.
Didier Deschamps' side, who thrashed rivals Paris Saint-Germain 3-0 last Sunday, followed up with a fine performance from the Ayew brothers although Stephane Mbia was injured four days before their decisive Champions League trip to Borussia Dortmund.
Marseille went ahead on 21 minutes when Morgan Amalfitano's shot at the near post was parried by Alexis Thebaux into the path of Andre Ayew, who poked the ball into the empty goal.
It took Caen only two minutes to equalise as Pierre-Alain Frau converted a penalty following a foul by goalkeeper Steve Mandanda on Livio Nabab.
Jordan Ayew made it two for the visitors seven minutes into the second half when he latched onto a Souleymane Diawara cross to slot the ball past Thebaux.
Cameroon midfielder Mbia went off with an ankle injury shortly before the hour and it was unclear if he would be fit for Tuesday.
He was replaced by Benoit Cheyrou, who helped the visitors keep the ball and preserve Marseille's slim advantage.
Striker Andre-Pierre Gignac, who was sent to train with the reserves last week after a spat with Deschamps but rejoined the first-team squad on Wednesday, came on as a 77th-minute substitute for Jordan Ayew but failed to make an impact.
