Rene Girard's men remain in the UEFA Champions League spots in third, but are now just one point above fourth-placed Saint-Etienne and are 13 adrift of league leaders Paris Saint-Germain.
Mathieu Bodmer's strike in first-half injury time was enough to complete victory at the Allianz Riviera, moving the hosts up to ninth.
Lille have now gone five matches without a victory in France's top flight, and will be keen for a swift response at home to Sochaux next Saturday.
Dimitri Payet and Mathieu Valbuena scored either side of Wissam Ben Yedder's leveller, as Marseille led 2-1 at half-time at the Stade Velodrome.
But Etienne Didot equalised on the hour mark as Alain Casanova's side left with a share of the spoils.
Lyon's three-match winning run in Ligue 1 ended at the Stade de la Route de Lorient.
Cedric Hountondji had fired the hosts into a 22-minute lead, while Samuel Umtiti's straight red card four minutes before the break further hindered Lyon.
