The Seagulls needed a result away in France after a 3-2 defeat against AEK Athens in their first ever European outing.
Early in the first half against Marseille, Brighton's defensive woes came back bite them as Chancel Mbemba scored an easy opener.
Just moments later, a mistake from Lewis Dunk allowed the hosts to double their lead though Jordan Veretout.
Roberto De Zerbi's side had chances to pull one back before the break but it was their second half performance that saved them.
In the 54th minute, Pascal Gross found the back of the net from the middle of the area to spark the Seagulls into life.
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As the clock ticked down it looked as though Marseille would hold onto their lead despite their opponents' resurgence.
However, Tariq Lamptey was brought down inside the box with just minutes remaining to award Brighton a penalty.
Joao Pedro, who scored their first ever European goals against AEK Athens, stepped up and slotted past Pau Lopez.
He scored his goal in front of the Marseille ultras and put his fingers to his ears as Brighton closed in on the draw.
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The result could prove to be a huge point for the Seagulls after their opening matchday defeat.
Brighton remain winless in three games across all competitions and have no conceded nine goals.
However, their chances of progressing to the Europa League knockout stages have received a huge boost thanks to their well-earned comeback in Marseille.