The Seagulls were assured of a place in the knockout stages of the competition before kick-off on the South Coast, however Joao Pedro's 88th-minute winner ensures that Roberto De Zerbi's men will qualify straight into the round of 16.
Gennaro Gattuso's side opted for an uncharastically-defensive approach considering that they only required a point to top the section, although Pedro's fifth of the continental campaign means that Les Olympiens will have to battle through a two-legged playoff in February.
Brighton made six changes to the side which drew 1-1 against relegation-threatened Burnley on the weekend, with Facundo Buonanotte and Kaoru Mitoma earning starts in the attacking line as Irish international Evan Ferguson and former England international Adam Lallana dropping to the bench.
Marseille opted to bring Ivorian Bamo Meite back into their XI at the expense of centre-back Samuel Gigot, but apart from that alteration it was an unchanged side from the one which earned the French club's first Ligue 1 away success of the season at Lorient on Sunday evening.
The Seagulls - needing a maximum on the South Coast to secure their spot as group winners - assumed control of the contest in terms of possession from the outset, with the likes of Billy Gilmour and Pascal Gross looking to dominant a Marseille engine room of Moroccan Azzedine Ounahi and Jordan Veretout.
Les Olympiens were working strictly on the break in the first period and found the most joy down the right-hand side through wing-back Jonathan Clauss, who has excelled at Marseille and whilst at former club Lens when given the chance to abandon his defensive responsibilities at points.
The France international fired a shot towards the goal of Jason Steele, however the strike took a massive deflection off Gross, meaning the ball looped furiously into the South Coast air, rattling off the crossbar and away from danger.
Unlike in their domestic matches, Gattuso's men were proving to be a tough nut to crack defensively on their travels this time around, and apart from a few fleeting moments of attack from the Seagulls in the first period, Pau Lopez's men was never truly threatened in the opening 45.
Despite their inferiority in terms of possession, Marseille went extremely close to hitting the front on the 60th minute, when winger Amine Harit saw his driven effort cannon off the post of Steele's net, before the 33-year-old keeper was hit by the rebound - luckily for the Seagulls Jan Paul van Hecke was on hand to clear the ball away from the onrushing Pierre-Emerick Aubameyang.
Pushing for the victory which would see them top the group, De Zerbi introduced Evan Ferguson, James Milner and Adam Lallana in the closing stages of the contest to help find a breakthrough, however it was the Seagulls' Brazilian starlet who secured maximum points in the final moments.
Former Liverpool man Lallana laid the ball into the path of engine-room partner Gross, who pierced a pass through to Pedro just inside the box, and the 22-year-old shifted the ball onto his preferred right foot before firing a shot into the top-left corner, sending the 30,000-plus crowd into hysterics.
In a group that contained French giants Marseille and four-time European champions Ajax, Brighton have clinched top spot during their first-ever continental campaign, collecting 13 points from six matches and winning their last four games in the competition without conceding a goal.
Looking to build on a magical night at The AMEX, the Seagulls travel to title-chasing Arsenal on Sunday afternoon, with the South Coast club currently eighth in the Premier League standings.
Marseille will find out their playoff opponents during Monday's knockout stage draw, but before that Les Olympiens are back in Ligue 1 action against strugglers Clermont Foot on the weekend.