Bakari Kone, Jimmy Briand and Alexandre Lacazette were on target for Les Gones, who had already secured a place in next season's Europa League thanks to their Coupe de France triumph.
Lyon are now six points ahead of Rennes and St Etienne, who lie in fifth and sixth respectively, with just two games remaining. Remi Garde's side have a superior goal difference of plus seven over Rennes and eight on St Etienne.
The visitors were made to work hard by Evian, who took the lead through Yannick Sagbo's volley after a quarter of an hour of play.
Lyon equalised just eight minutes later though, Kone nodding home Yoann Gourcuff's corner before they took the lead on 68 minutes, Briand with an easy finish after keeper Stephan Andersen punched into his path.
Evian pressed for a leveller of their own late on, Mohammed Rabiu hitting the bar, but victory was sealed by Lyon when Lacazette scored from the penalty spot after he was brought down by Cedrid Cambon in the box.
Evian remain in ninth place in their first season in the top flight following from Ligue 2 as champions.