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:
9. Solly March - 6
Unable to make space for himself in the first half, largely controlled by the hosts. March didn’t look a threat until he fired an effort wide on the stroke of half-time. Improved with the team after the break and played his part in a stirring comeback Photo: NICOLAS TUCAT/AFP via Getty Images
10. Kaoru Mitoma – 6
Looked out of sorts against Aston Villa on Saturday and he was anonymous in the first half again today. But the Japan international was much improved after the break and provided a nice assist for Gross. Showed great pace and had a good shot saved. Lovely turn but pass slightly behind Adingra. Photo: NICOLAS TUCAT/AFP via Getty Images
11. Ansu Fati - 5
Still waiting to see the Barcelona loanee show his best in Brighton colours. Couldn't quite get the ball down to shoot in a good position early on. Excellent headed effort brilliantly saved. Would've had a tap-in if Welbeck squared it on the stroke of half-time Photo: NICOLAS TUCAT/AFP via Getty Images
12. Danny Welbeck - 5
One of the few players with European experience in the team and he struggled. His hold-up play wasn't at his best and his attempts at goal were wayward. Wasted a huge chance on the brink of half-time when he had a tame shot saved when he should have squared it to Fati who would've had a tap in. Passing improved as Brighton started to control possession. Photo: Mike Hewitt / Getty Images