Marseille, who surged ahead through first-half goals by Benoit Cheyrou and Brandao, remained fifth with 38 points from 22 games, 11 behind leaders Paris Saint-Germain who beat Evian Thonon Gaillard 3-1 on Saturday.
Lyon, who fought back thanks to Bafetimbi Gomis and a Souleymane Diawara own goal before half-time, stayed fourth on 39 points.
Second-placed Montpellier, three points off the pace, also won on Saturday, beating Stade Brest 1-0 as champions Lille, who have 39 points, had their game at Sochaux postponed because of a frozen pitch.
Two other matches were called off over the weekend and the French League still has to decide when the Lille game, as well as Saint-Etienne v Lorient and Caen v AJ Auxerre, will be played.
The hosts, on a four-match winning streak in Ligue 1, were without the suspended Mathieu Valbuena as well as the Ayew brothers, Andre and Jordan who are on Africa Cup of Nations duty with Ghana.
Marseille went ahead on 16 minutes when Cheyrou volleyed home following a bad clearance by the Lyon defence.
Brandao tapped in from a Morgan Amalfitano cross to double the tally in the 34th minute but Lyon fought back against the run of play.
With a clever backheel, Jimmy Briand sent the ball into the path of Bafetimbi Gomis who fired home at point-blank range to reduce the arrears two minutes later.
On the stroke of half-time, Souleymane Diawara, who returned to Marseille this week after Senegal were eliminated from the Africa Cup of Nations deflected an Aly Cissokho cross into his own goal.
In the closing stages, Marseille keeper Steve Mandanda made a lightning quick save from Lisandro Lopez to help his team extend their unbeaten run to 13 games in all competitions.
