It was a blow for Andre Villas-Boas' side whose victory against bitter rivals Paris Saint-Germain at the weekend took its toll, as forward Dario Benedetto and left-back Jordan Amavi were suspended after being sent off in a brawl at the end of the bad-tempered match in the capital.
Defender Alvaro Gonzalez, at the centre of allegations that he racially abused PSG's Neymar on Sunday, did start.
Only around 1,000 spectators were present at the Stade Velodrome due to coronavirus restrictions.
Les Verts move to the top of the table with the three points as Claude Puel's men remain unbeaten this season.
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 fell 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 to end the 41-year wait by firing past Steve Mandanda with 11 minutes to play.