Capitalising on Paris Saint-Germain's draw on Saturday, the home side was able to open up a three point gap heading into the new year.
An own goal from Nolan Roux gave the home side a deserved lead at the Stade Velodrome, before Idrissa Gueye leveled matters in the second half. However, Belgian youngster Michy Batshuayi popped up in the 69th minute to net the winning goal.
The victory sees Marcelo Bielsa's men open up a three point lead atop of the French top-flight after Paris Saint-Germain drew 0-0 with Montpellier on Saturday.
The home side started the game well, creating several chances against a stuttering team which sits 13th in the table.
Andre-Pierre Gignac could have given his side the lead 12 minutes in when Simon Kjaer's poor clearance from a cross fell to the striker who had acres of space in the box. Instead of bringing it down, though, the France international chose to hit a shot and it spun wide.
Kjaer handed the home side another chance when another attempted clearance from Kjaer bounced to Andrew Ayew, but the center back was able to recover and knock it out for a corner.
Marseille took the lead shortly after the half hour mark when Florian Thauvin sent a corner low and toward the front post. The cross was a poor one, but Lille defender Roux came to clear it and the defender led with the wrong foot and ended up diverting it into his own net.
After a slow start to the second half in which Marseille had eased up on the pressure, Lille pushed forward and looked brighter, eventually equalizing 15 minutes after the restart.
The ball was played out wide as the club looked to exploit Marseille's high defensive line before being knocked into the box for Djibril Sidibe, who held it up and squared to Gueye who slammed it home with the aide of a deflection.
For the most part, Lille was restricted to efforts from long range, with Divock Origi, Gueye and Rio Mavuba seeing tame efforts stopped by Steve Mandanda.
That wastefulness was capitalised on by Marseille as the lead was restored shortly afterwards. Michy Batshuayi took on a Thauvin cross, turning and holding off Marko Basa and blasting it past Vincent Enyeama.
Lille began to push forward once again in an attempt to try and steal a draw, but failed to make the difference and Marseille ensured it stayed top of the table.