Marseille quickly took control of the rescheduled game at the Stade Velodrome against a Lyon team that was put under pressure right away.
The match came just four days after the death of a fan ahead of a French league game that marked a new low in a season marred by violence.
The Marseille-Lyon game was initially scheduled on Oct. 29, but was postponed after fans threw rocks and other projectiles at the Lyon bus and then-coach Fabio Grosso needed stitches in his forehead after being hit by broken glass.
Lyon fans were not allowed to travel to the rescheduled game, which took place in a fervent but peaceful atmosphere.
Portuguese striker Vitinha put the hosts in front in the 20th minute from Aubameyang's cross with a left-footed shot.
Michael Amir Murillo made it 2-0 four minutes later after Aubameyang broke down the left and passed the ball at the far post for his unmarked teammate, who headed it home past Lyon goalkeeper Anthony Lopes.
Aubameyang then turned from provider to scorer in the 54th minute from Vitinha's precise back pass.
After a mediocre start since joining this summer, Aubameyang has found a new lease of life. He scored a hat trick against Ajax last week in Europa League and had one goal against Rennes over the weekend.
Both Marseille and Lyon, two traditionally successful French clubs, have struggled this season. The win moved Marseille to eighth place in the standings, 13 points behind leader Paris Saint-Germain. Lyon is bottom of the league with just one win and nine losses in 14 matches.