The 124th derby between the bitter rivals did little to suggest either that Lyon can force their way into contention for a European place or that Saint-Etienne can escape the foot of the Ligue 1 table.
Lyon climbed to 10th, six points behind third-place Marseille, ahead of the rest of the weekend fixtures.
Saint-Etienne's seventh straight loss left them six points away from safety.
Lyon will face sterner tests in the coming week as they take on five teams above them: Marseille, Monaco, Nice, Lens and Lille.
Health restrictions meant the derby was played in front of just 5,000 spectators in a stadium that holds 60,000.
Even at home against the last place team, Lyon played Dembele as a sole striker but he did just enough to win the game.
Dembele was brought down by Timothee Kolodziejczak in the 15th minute and then converted the penalty.