Lille took the lead after 17 minutes when Jonathan David seized on a short pass back to round the goalkeeper and roll the ball into the empty net.
The Canadian's 12th goal of the season was also his ninth in his last eight club matches.
Lille should have added to their total in a dominant first half but the post and their failure to capitalize opened the door for Lyon to storm back in a blistering second 45 minutes.
Rayan Cherki saw his shot hit the bar and Ainsley Maitland-Niles had a goal chalked off after a video review before the equaliser.
In the first minute of stoppage time, Maitland-Niles' pace proved decisive. He got away from his marker and sent over a cross for Fofana to volley home.
The result meant both teams rose one place in Ligue 1 - Lille to third and Lyon to fifth.
Earlier, a spectacular first-half strike by Jean-Eudes Aholou gave Angers a 1-0 win at Monaco.
After an 11-game winless streak dating to July, Angers have won two in a row for the first time since May.
Friday's victory lifted them into 14th place in the 18-team league.
The story for Monaco is almost a mirror image of Angers' rise. The club from the principality have lost two in a row after a 12-game unbeaten run from the start of August to the end of October.
They were missing a host of regulars in a game that was lifted by Aholou's wonder strike after 29 minutes.
The Ivory Coast striker took a short pass from Jim Allevinah and lashed a left-foot strike that gave goalkeeper Radoslaw Majecki no chance.
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