Defeat sees Les Dogues miss the chance to go level on points with Paris Saint-Germain at the top of Ligue 1.
Both teams started the encounter brightly, but struggled to create anything going forward.
The deadlock was broken in the 22nd minute when Gregory Bourillon headed home Yann Jouffre's free kick.
Lille pushed forward after the break, searching desperately for an equaliser, with Dimitri Payet guilty of missing their best opportunity in the 55th minute.
Despite their best efforts to get back into the game, Benjamin Corgnet slammed in a second for the hosts with 20 minutes to go to seal the points.