But Gillingham made it four home wins in a row to jump three more places up the First Division table and leave themselves on the fringe of the play-offs.
They completed the double over Steve Coppell's side with three second-half goals from Paul Shaw, sub Tommy Johnson and Nicky Southall.
Mamady Sidibe was foiled by two early saves at his feet by Brighton goalie Dave Beasant just days off his 44th birthday.
Beasant then did well to stop another effort from Nayron Nosworthy as the game started at a lively pace on a poor pitch made even worse by Friday's heavy downpours.
Sidibe pulled up quickly and could not continue so Johnson got an early call from the bench to face a side he scored twice against for Notts County in the play-offs more than ten years ago.
Gillingham took time to adjust and Brighton stuck to the task well with Tony Rougier and Graham Barrett giving Gills central defenders Chris Hope and Barry Ashby plenty to think about.
Another worry for Gillingham was Paul Smith feeling his hamstring just before half time, and he needed a fitness check from the club doctor at half time before resuming.
The home side made the perfect start after the half-time interval.
The ball found Shaw on the right and Rod Wallace continued to move setting up Johnson, whose shot was parried by Beasant, but only fell nicely to Shaw who headed in at the far post.
Then Brighton missed a great chance to equalise when Smith left his backpass short, but Rougier and Barrett failed to make anything of it and Gillingham breathed easy again.
Johnson then created the opening for a second goal. He slipped past defender Ivar Ingimarsson, whose challenge floored the Gillingham striker leaving ref Peter Walton to point to the spot.
Johnson stepped up send Beasant the wrong way and gave Gillingham a two-goal lead.
Gillingham made sure a victory was the third nine minutes from time when Southall fired home a loose ball after Shaw's initial shot had been blocked.