Knowing a win could yield them a top 24 spot, Brugge got off to a blistering start with two goals inside the opening 11 minutes.
Aleksandar Stanković played through Mamadou Diakhon for the first, as he slotted calmly into the corner, before the Serbian then provided again for Romeo Vermant, who volleyed brilliantly in off the post.
A man determined to wreak havoc, Diakhon troubled Marseille’s defence again soon after, but after going on a mazy run, Gerónimo Rulli saved well.
Meanwhile, Mason Greenwood was on a solo mission to get his side back in it before half time, with Simon Mignolet denying him on three separate occasions.
Unsurprisingly, Marseille's boss made early changes in the second half, including bringing on talisman Pierre-Emerick Aubameyang.
He almost made an immediate impact, forcing Mignolet to parry away his powerful strike. Igor Paixão then had a further effort thwarted by the Belgian, as the visitors struggled to find the breakthrough they desperately needed.
After that, Rulli prevented Stanković from putting the game to bed down the other end with a decent save, but the goalkeeper could not stop him a second time as he scored his sixth goal in seven appearances with a fine finish into the bottom corner.
That ensured Club Brugge's progress, while Marseille were now entirely reliant on events in Lisbon to seal progression.
But with a remarkable last-minute goal by Benfica goalkeeper Anatoliy Trubin against Real Madrid, Marseille's fate was sealed at the very last moment of what was an incredible Matchday Eight across the continent.
Flashscore Man of the Match: Aleksandar Stanković (Club Brugge)
