The build-up to the game was focused on former Marseille boss Rudi Garcia's return to the Stade Velodrome after his controversial decision to join Lyon as coach, but it is more likely to be remembered for ugly scenes off the pitch.
Home supporters attacked the Lyon bus with stones, bottles and other projectiles on its way to the stadium, before visiting players were repeatedly bombarded with objects thrown from the crowd while taking corners during the match.
Payet netted a first-half double as Marseille moved second in the Ligue 1 table, eight points adrift of Paris Saint-Germain.