CSKA defender Vasily Berezutsky skewed the ball into his own goal shortly after the break to put the visitors ahead.
Moussa Sow sealed his team's first win in the group midway through the second half, tapping into an empty net after Joe Cole's shot hit the post.
Lille's victory meant group leaders Inter qualified for the first knockout round in February with nine points regardless of the result of their match at Trabzonspor on Tuesday, which finished 1-1.
The French champions are now level with CSKA and Trabzonspor on five points with one set of matches left to play and the top two going through.
The Russians sorely missed top scorer Seydou Doumbia, whose late double enabled them to snatch a 2-2 draw in Lille in their first meeting in September.
DOUMBIA BAN
The Ivory Coast striker has been on fire since joining CSKA last year with 11 goals in 11 European games for the club.
Doumbia, who also notched up 24 goals to lead the Russian league's scoring charts this season, was serving a one-game ban after being red-carded in their previous game against Trabzonspor.
CSKA, decimated with injuries to many of their key players this season, suffered another blow on the eve of Tuesday's match when midfielder Keisuke Honda was ruled out with a knee problem.
The Japan international, who had just returned to CSKA's lineup in a league game after missing more than three months with torn ligaments in his knee, aggravated the injury in training on Monday.
Without their creative players, the Russians looked toothless in front of the goal for most of the match -- their lone Brazilian striker Vagner Love unable to pose much of a threat.
Lille dominated in the first half but wasted several chances, midfielder Cole shooting straight at CSKA keeper Vladimir Gabulov and defender Mathieu Debuchy hitting the bar from close range.
Franck Beria just fired wide from a sharp angle after Gabulov blocked Sow's shot.
