Eurosport - Supporters OM Stade Vélodrome
The win cemented their position at the top of Group 6 in the NextGen Series.
The sides were evenly matched throughout the game, and it needed a touch of class from Antoine Kisaku to settle the contest.
He slotted past Deylan Iliev three minutes into injury time to secure all three points for the home side.
Marseille travel to Greece next month to face Olympiacos whilst Arsenal face Athletic Bilbao in November.
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