Laurent Blanc collected just a single point from his first two games in charge and was left thanking Ezequiel Lavezzi's second-half strike for ensuring he got into the winner's circle.
Summer signing Edinson Cavani fired the champions ahead before Alex's own goal levelled matters just after half-time.
Lille forward Solomon Kalou scored the only goal of the game to end St Etienne's perfect start to the season.
The former Chelsea man's first-half penalty was the first league goal conceded by Les Verts this season and it was enough move the hosts level on points with them in the table.
Ajaccio's winless start continued as they were held to a goalless draw by Nice at the Stade Francois-Coty.