The Gunners went into the match full of confidence having comfortably defeated the French outfit 3-0 in August's reverse fixture.
However, on this occasion they were largely dominated by Marseille, who struck the crossbar either side of the break.
The home side then thought they had won it when they netted with five minutes remaining, but Junior Anani's effort was ruled out for a foul on the goalkeeper.
That didn't prove to be costly though as substitute Kisaku snatched Marseille victory with the last kick of the game.
Arsenal sit third in NextGen Group 6 with four points, while Marseille top the pool with seven.