Quickfire goals from Chancel Mbemba and Jordan Veretout in the first-half left Albion facing a damaging defeat but the visitors were much-improved after the break.
Pascal Gross – who was making his return from injury – got one back on the 54th minute, before Joao Pedro scored his third goal of the European campaign with his third penalty two minutes before stoppage-time.
Albion remain bottom of Group B after two games but are just one-point behind second-placed Marseille, and three behind Athens, who drew 1-1 against Ajax.
The Seagulls looked sluggish early on, seemingly still suffering from the effects of the 6-1 defeat at Aston Villa and dealing with an unfamiliar intense atmosphere in France.
The defenders were too static as former Newcastle defender Mbemba opened the scoring after 19 minutes. The hosts added a second just a minute later after a huge mistake by skipper Lewis Dunk was punished by Veretout. Jason Steele could have done more to keep the ball out.
Brighton responded well and they thought they had a penalty after the referee was told to check for a handball. He appeared to point to the spot after watching several replays but no penalty was forthcoming – much to the confusion of fans in the stadium and those watching at home.
The visitors kept up the pressure and should have scored before half-time.
They continued where they left off after the break and got the goal they deserved. It was the returning Gross who found the net from Kaoru Mitoma's pass after great work by Tariq Lamptey.
Marseille had lost the momentum and control of the game and it seemed a matter of time before Brighton would find an equaliser.
They had to wait until the 88th minute when Pedro kept his nerve once again to send the keeper the wrong way from the spot.
Scroll down and click through to see how we rated Roberto De Zerbi’s players:
5. Lewis Dunk - 6
Will be having nightmares about his error which led to the second goal on his European debut. Put a header over the bar from a corner as he tried to make amends. Make amends he did with a sensation block to deny Vitinha a certain goal at a crucial moment in the game. Looked more assured of himself after the break. Booked. Photo: NICOLAS TUCAT/AFP via Getty Images
6. Tariq Lamptey - 8
Played left back in Pervis Estupinan's absence. Struggled early doors but quickly became Brighton's best performing player. Hard but fair challenge on Harit rightly deemed as such. Superb determination in build up to Gross' goal. A real thorn in Marseille's defence and was the spark that led to the come-back. Won the crucial penalty late on after a burst into the box. Superb performance Photo: NICOLAS TUCAT/AFP via Getty Images
7. Mahmoud Dahoud - 5
Didn't cover himself in glory while defending for the first goal. Struggled to take control of the midfield. One standout moment was a superb pass to Fati which nearly led to a goal. Replaced with more than 20 minutes remaining Photo: Tim Nwachukwu/Getty Images
8. Pascal Gross - 7
Scored on his return from injury. It was a composed finish and he once again proved to be a big game player. A tad sloppy in moments as he works to get back to full fitness Photo: Mike Hewitt/Getty Images