Paris Saint-Germain had opened up a one-point advantage after Saturday's 3-1 win at Nice, but Hubert Fournier's men went back to the summit on goal difference after a thrilling Rhone-Alpes Derby.
Clinton N'Jie opened the scoring 24 minutes in, only for Max Gradel and Romain Hamouma to turn the game on its head following Lindsay Rose's dismissal for handling in the area.
Christophe Jallet restored parity with his first Lyon goal although PSG's game in hand will likely prove a concern for Fournier's side and their title aspirations.
Like Saint-Etienne, Lille and Montpellier will both fancy their chances of gaining a European berth having both picked up victories on Sunday.
Indeed, Sunday could prove to be a decisive day in the race for a top-four finish after Lille moved within four points of Bordeaux in sixth thanks to a 2-0 win over Willy Sagnol's side.
Nolan Roux set the hosts on their way to a third consecutive league success at the Stade Pierre Mauroy before Adama Traore made sure of the points in the final minute.
It briefly put Rene Girard's men into seventh although Montpellier's success against Caen made that a brief state of affairs.
Hilton's early goal proved the winner in a 1-0 success, with the race for European football continuing into the final five games of the season.
