Grimsby increased the pressure on Brighton manager Martin Hinshelwood with their first win of the season to send the South Coast strugglers to the bottom of the table.
Goals at the start and finish by Darren Barnard and Alan Pouton sentenced Brighton to their ninth straight league defeat after Bobby Zamora marked his comeback with an equaliser.
The victory ended a run of six defeats on the trot for Paul Groves' side and takes them a point above their victims.
Brighton conceded an early goal at home for the fifth match running as Barnard stroked the visitors into a second minute lead.
The former Barnsley midfielder ran on to a pass from on-loan Wimbledon forward Paul Robinson to beat Brighton's fit-again keeper Michel Kuipers at his near post.
Teenager Darren Mansaram, making his full debut for the Mariners, almost doubled their advantage with a low shot which hit a post.
Brighton huffed and puffed and eventually broke through with 19 minutes left. Zamora, picked out by Charlie Oatway, scored his second of the season from close range, on his return from a nine-match absence with knee ligament damage.
Alan Pouton thought he had restored Grimbsy's lead after 77 minutes with a fierce free-kick from the edge of area.
It was disallowed by ref Mark Warren because he had already blown to book Oatway for breaking from the defensive wall.
Paul Wilkinson, the Grimsby coach, was then ordered from the dugout by Warren, but Pouton had the last laugh.
Inspired by the injustice, he finished a strong run through the heart of the Brighton defence with a low drive from the edge of the box ten minutes from time.
Pouton said "Everyone was wound up by the referee's decision and that spurred us on."