Lyon, with 46 points from 23 matches, are four points ahead of Bordeaux, who squandered the opportunity to keep a tight rein on the leaders in Sunday's late game at the Stade Velodrome.
An own goal by Morocco striker Marouane Chamakh settled the match when he headed a Benoit Cheyrou free kick past his own keeper in the 57th minute.
Brazilian midfielder Wendel had an opportunity to level on the hour but his shot hit Steve Mandanda's right post before bouncing out off the Marseille keeper's head.
Bordeaux's woes continued in the 87th minute when defender Souleymane Diawara was sent off for a second bookable offence.
Marseille are fourth, five points off the pace and one behind Bordeaux and third-placed Paris St Germain, who thrashed Nantes 4-1 on Saturday.
In Nice, seven-times champions Lyon appeared on course for a straightforward win after early goals by Makoun and Karim Benzema but Onyekachi Apam reduced the arrears on the stroke of halftime.
Cameroon midfielder Makoun was perfectly set up by Brazilian Ederson to slot the ball home from close range on 17 minutes. Juninho lofted a cross above the Nice defence for Benzema to collect the ball and fire past David Ospina nine minutes later.
The hosts were lucky to pull one back in first half added time when Apam netted from close range from a Chaouki Ben Saada corner kick.
However, Lyon kept their composure in the second half as Nice, who had only lost once at home in Ligue 1 this season, gradually lost their temper - and had two players sent off.
Midfielder Julien Sable was the first go, shown a straight red card for a violent tackle on Ederson just before the hour.
Brazilian striker Adeilson, who came on as a 69th-minute substitute for his first Ligue 1 game, also received a straight red card six minutes from time for slapping Jean-Alain Boumsong in the face.
Lyon had a penalty after Ospina fouled Ederson but the Nice keeper parried Benzema's attempt.
Makoun headed home 10 minutes from time to wrap up the win.
