It was not so much a victory as a rout, as Puel celebrated his 600th Ligue 1 game.
Marseille, who were also defending a perfect start to the campaign, went into the match as slight favourites after their acrimonious 1-0 victory at Paris Saint-Germain on 13 September.
Defender Alvaro Gonzalez, at the centre of allegations that he racially abused PSG's Neymar on Sunday, started the game at the Velodrome where only 1,000 fans were permitted due to coronavirus restrictions.
Depleted Marseille
But without forward Dario Benedetto and defender Jordan Amavi - both sent off in a brawl at the end of the match at the Parc des Princes - Marseille had less bite in attack and steel in defence.
Veteran winger Hamouma broke the deadlock after six minutes, sidefooting home from Yvann Macon's low cross.
The home side's best chances to score came 10 minutes into the second half as 19-year-old Nathan Ake hit the crossbar and midfielder Morgan Sanson dribbled his effort past the post less than 60 seconds later.
Gabon international left-winger Bouanga doubled his side's lead with 11 minutes to play.
