Taking charge of his second game as Marseille boss, Gennaro Gattuso watched his side surge into a two-goal lead in the Europa League contest, after Jordan Veretout found the net within 90 seconds of Chancel Mbemba's opener.
Germany international Pascal Gross scored his first European goal within 10 minutes of the restart to give Brighton some much-needed impetus.
With time running out, the Seagulls salvaged a point in the 89th minute when substitute Joao Pedro stroked the ball home from the penalty spot after Tariq Lamptey was brought down in the box.
Despite clinching their first point in UEFA competition, Brighton finish matchday two bottom of Group B, while Marseille occupy second place after drawing their opening two group games.
After shipping six goals in Sunday's demoralising defeat to Aston Villa, the Seagulls got off to the worst possible start at the Stade Velodrome, conceding two quickfire goals which exposing their defensive frailties once again.
They fell behind in the 19th minute when Mbemba swept the ball home following a slick piece of interplay from Jonathan Clauss and Joaquin Correa on the right flank.
Just moments after taking the lead, the home faithful were celebrating a second goal after Lewis Dunk was punished for an error on his European debut.
The Brighton defender lost the ball in his own half, gifting possession to Amine Harit, who sent a low cross into the box for Veretout to squeeze under Jason Steele.
After leaving themselves with a mountain to climb, the Seagulls thought they had a lifeline when the referee appeared to point to the point following a VAR review, but it was ultimately deemed that a foul had been committed by Brighton before the ball struck a Marseille hand.
As the half progressed, Roberto De Zerbi's side began to trouble Pau Lopez in the Marseille goal, with Ansu Fati and Danny Welbeck forcing the goalkeeper into action.
Solly March then fired wide in first-half stoppage time, ensuring the Ligue 1 outfit took a comfortable two-goal lead into the interval.
After finishing the first half on the front foot, Brighton utilised that momentum to make a positive start to the second period thanks to Pascal Gross's 54th-minute strike.
The 32-year-old was on hand to guide the ball past Lopez from Kaoru Mitoma's neat cut-back to give the Seagulls a crucial foothold in the contest.
Mitoma looked to turn from provider to scorer when he raced through on goal in the final 20 minutes, but his left-foot strike was pushed away by Pau Lopez.
Brighton's quest for the all-important equaliser looked set to end in disappointment before Lamptey earned a penalty following a clumsy challenge from Clauss.
Pedro shouldered responsibility from the subsequent spot-kick, keeping his composure to send the goalkeeper the wrong way and register his third goal in two Europa League appearances.
After avoiding a third straight defeat in all competitions, the Seagulls will try to build upon their impressive second-half display in Sunday's Premier League meeting with Liverpool, while Gattuso will attempt to claim the first win of his tenure when Marseille face Le Havre this weekend.