Simon Kjaer and Salomon Kalou both had early chances for the visitors, while Florent Balmont had an effort from range which just missed the target.
Kalou had a series of chances just before the break, before Renaud Cohade tested the Lille keeper with a 25-yard strike for the home side.
After a quiet start to the second half, Lille continued to create the majority of the chances, but it was Saint-Etienne who broke the deadlock, with Brandao heading in from close range following a Faouzi Ghoulamcross.
Nolan Roux almost got the visitors back on level terms within two minutes, but his left-footed strike from saved.
The hosts were able to double their lead shortly after though, when Romain Hamouma's shot was parried into the path of Franck Tabanou, who was left with an easy finish.
The situation got worse in the aftermath of the goal, as Balmont blamed the referee for not spotting a foul in the build up to the goal, earning him a red card.
Brandao came close to bagging a brace, testing Vincent Enyeama with a long-range effort, but the Lille keeper was able to make the save late on.
The results closes the gap between between the fourth-placed hosts and Lille, who sit third in the table.
