Nabil Fekir and Mariano Diaz struck each side of the interval to put OL on 38 points from 18 games, three points ahead of fourth-placed Marseille.
Monaco are second, above Lyon on goal difference, after they thrashed St Etienne 4-0 away on Saturday (AEDT).
Paris Saint-Germain are the runaway leaders with 47 points after their 4-1 win at Rennes.
Lyon took the lead after just six minutes when Steve Mandanda failed to handle Fekir’s 35-metre free-kick as the hosts got off to a dream start.
Marseille had lost only one of their last 15 away games in Ligue 1, and they still dominated with Valere Germain coming close on two occasions.
The hosts, however, held them off until the interval and could feel lucky they had a one-goal advantage at the Groupama stadium as they only had one shot on target.
Lyon goalkeeper Anthony Lopes was instrumental in his team’s performance as he produced several first-class stops.
Mandanda also made a super save but parried the ball into the path of Benjamin Cornet who crossed for Diaz, who doubled Lyon’s tally six minutes into the second half.
The Provence side now lead fifth-placed Nantes by five points.
