A fortuitous goal nine minutes from time settled the Group B contest after both sides saw chances go begging earlier in the match.
Nathan Oduwa went down in Marseille’s penalty box just four minutes into the match in Ploufragan, but the referee was unmoved.
Goalkeeper Harry Voss denied Maxime Lopez in a one-on-one situation shortly afterwards, before Jon Obika skewed a shot off target at the other end.
Josh Onomah and Emmanuel Sonupe later combined to cause Marseille problems, but it was the French side who took the lead when Fabrice Apruzesse capitalised on a defensive slip and fired past Voss.
Sonupe was denied in his attempts to swiftly restore parity, while Ruben Lameiras produced a stop from Marseille goalkeeper Florian Escales in the closing moments as we chased an ultimately elusive equaliser.
Academy Manager John McDermott, who joined our new Under-21 coach Ugo Ehiogu in the dugout, said: "The match was played against several wily old pros in what was a great environment to learn.
"We stood up well to our opponents' physicality and had more chances than Marseille, with some outstanding passages of play.
"Cameron Carter-Vickers was the youngest player on the pitch but set the example with his defending and concentration. Josh Onomah was the pick of the bunch in the middle of the pitch and Emmanuel Sonupe continued his good pre-season form with some relentless attacking play."
The result leaves us with work to do in our matches against Lorient (11am local time) and Guingamp (6.30pm local time) on Saturday.
Spurs: Voss, McQueen, Walker-Peters, Winks, Carter-Vickers, Lesniak, Sonupe, Onomah, Obika, Oduwa, McEneff.