Joao Pedro scored an 88th-minute winner to help Brighton advance to the Europa League last 16 stage.
Having started the final round of group matches one point behind Marseille, only a win for Brighton would have helped them avoid a potentially difficult play-off tie.
But for 87 minutes their French opponents, who are sixth in Ligue 1 having won each of their past four league fixtures, defended with discipline and created the match's better chances.
They struck the bar early in the first half when Jonathan Clauss' shot deflected off Pascal Gross and looped over Brighton keeper Jason Steele, only to bounce out off the woodwork.
And, after the restart, Amine Harit's low shot hit the base of the Brighton post, but no Marseille player was nearby to tap in the rebound.
The Seagulls, despite dominating possession, had been limited to half chances with Pedro meeting a low cross with a driven effort off target and Billy Gilmour having a shot from range easily saved.
Evan Ferguson came close late on minutes before Pedro's winner when his powerful strike from the edge of the box was tipped over the bar by goalkeeper Pau Lopez.
Brighton XI: Steele, Gross, Dunk, Igor, Kaoru Mitoma, Gilmour, Jan Paul van Hecke, João Pedro, Simon Adingra, Facundo Buonanotte, Jack Hinshelwood
Subs: Milner, Lallana, Veltman, Dahoud, Tom McGill, Evan Ferguson, Bart Verbruggen, Samy Chouchane, Jack Hinchy, Carlos Baleba, Leigh Kavanagh, Josh Duffus
Marseille XI: Aubameyang, Jonathan Clauss, Veretout, Mbemba, P. Lopez, Harit, Lodi, Balerdi, Azzedine Ounahi, Vitinha, Bamo Meïté
Subs: Kondogbia, Blanco, Samuel Gigot, M. Murillo, Sarr, Iliman Ndiaye, Ngapandouetnbu, Bilal Nadir, Emran Soglo, François Mughe
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