Belgian striker Michy Batshuayi netted a half-volley in the 69th minute as Marseille ensured they stayed top of the table heading into the two-week winter break.
Batshuayi, who was given the nod ahead of Dimitri Payet after the Frenchman was dropped by coach Marcelo Bielsa due to poor training performances, controlled Florian Thauvin's cross before turning and firing the ball into the top corner of the net.
The match-winner came eight minutes after Idrissa Gueye equalised for Lille, cancelling out Marseille's first-half opener at the Stade Velodrome.
Marseille hit the front fortuitously in the 32nd minute when Lille's Nolan Roux sent the ball into his own net.
Bielsa's Marseille enjoy a two-point buffer atop the table, ahead of Lyon, who were big winners on Sunday as they leapfrogged defending champions Paris Saint-Germain into second spot.
Bordeaux were reduced to 10 men in the 65th minute when Nicolas Pallois was sent off for a challenge on Clinton N'Jie.
