Gomis, who grabbed a hat-trick in the 4-1 win at Olympique Marseille on Wednesday, fired the ball in from just outside the box in the 26th minute.
Lyon have 31 points from 15 games, five ahead of second-placed St Etienne who drew 0-0 at Ajaccio on Friday. Paris St Germain, also on 26 points in third spot, visit Nice later on Saturday.
Inspired by in-form Clement Grenier, the Ligue 1 leaders outclassed Montpellier in the first half and denied them any goal chances.
The 21-year-old playmaker laid on the only goal when he took possession in his own half before setting up Gomis who netted with a powerful effort.
Grenier went close to making it 2-0 when his curling 34th-minute free kick was saved by debutant goalkeeper Jonathan Ligali as it arrowed towards the top corner.
Montpellier, who are down in 12th spot and had scored in their 12 previous away league matches, pushed hard for an equaliser but could not make the breakthrough. (Reporting by Gregory Blachier; editing by Tony Jimenez)