There were wild celebrations in the stands as Joao Pedro struck a late winner to send Albion top of their group above Marseille.
Only a win would do for Roberto De Zerbi’s side to win their Europa League group and go straight into the round of 16 in March.
Marseille needed to avoid defeat to top the group.
But in an intense atmosphere, Brighton continued to knock on the door and eventually broke through with a sumptuous one touch passing move which Joao Pedro slammed into the top corner with just two minutes remaining.
The Brazilian rushed towards the East Stand and jumped into the mass of celebrating Albion fans.
Marseille failed to register a shot on target in the match although came close with efforts which struck the bar and post.
One shot in the first half deflected up and almost looped over Jason Steele but came off the cross bar.
While in the second half, another effort came off the post and bounced off Jason Steele before being cleared by Jan Paul van Hecke.
Brighton controlled possession but struggled to keep their shots on target.
Brighton qualified for the round of 16 along with West Ham, Rangers, Atalanta, Liverpool, Slavia Prague, Bayer Leverkusen and Villarreal.
The draw will be on February 23 and the two legs will be on March 7 and March 14.
Comments: Our rules
We want our comments to be a lively and valuable part of our community - a place where readers can debate and engage with the most important local issues. The ability to comment on our stories is a privilege, not a right, however, and that privilege may be withdrawn if it is abused or misused.
Please report any comments that break our rules.
Read the rules here