A controversial 39th-minute penalty by David Lopez condemned Millwall to a second successive defeat as the promotion chasing Seagulls swooped to steal three points at The Den.
There seemed to be minimal, if any contact, by Lions skipper Danny Shittu in the 39th-minute as the defender went shoulder to shoulder with Brighton debutant Jesse Lingard in the penalty area.
However, Lingard fell dramatically to the deck and was adjudged to have been fouled by Shittu, who like the rest of The Den faithful, was aghast when referee Geoff Eltringham pointed to the spot.
Lopez stepped up and promptly despatched the penalty kick into the bottom left corner, sending Lions keeper David Forde the wrong way to hand the visitors an advantage they had to battle expertly to defend.
It had all started reasonably well for boss Ian Holloway, who handed a debut to new signing Owen Garvan - the 40th player used by The Lions this season.
Garvan's inclusion was one of three changes to the team that started at Barnsley last weekend, with Jermaine Easter and Simeon Jackson brought in for Scott McDonald and Steve Morison.
There were three minutes on the clock when Ed Upson, who was a dominant feature in the Millwall midfield, nearly caught out Seagulls keeper Tomasz Kuszczak with a free-kick from the left that landed on the roof of the net.
Five minutes later another Upson effort, this time from the other flank, was comfortably collected the Kusczak before the visitors recorded their first real noteworthy attempt on goal in the 10th-minute, only for Dale Stephens' tame 25-yarder to bounce wide of the post.
Millwall had a huge let-off midway through the half when Andrea Orlandi broke down the left and whipped over a delightful ball that was met by the head of Jose Ulloa, but his effort was gathered at the second attempt on the line by keeper Forde.
Upson again was denied with a thumping drive from 25-yards that stung the palms of the Seagulls keeper, but it was Brighton who went on to break the deadlock six minutes before the interval with the controversial penalty that also earned Shittu a yellow card for his protests.
The Seagulls went close to adding a second goal moments before half-time, only for a strong block by Ryan Fredericks to divert Lingard's goalbound shot.
Boss Holloway made no changes at the break and his faith was nearly repaid immediately when Shittu's close-range header from Garvan's sweet free-kick went straight into the arms of the grateful keeper.
Easter was a whisker away from grabbing a deserved Lions leveller just before the hour-mark only to see his close-range effort smack the crossbar.
That proved to be the striker's last contribution of the afternoon as Morison and McDonald were brought on in a bid to try and unlock a resilient Seagulls rearguard.
McDonald fired over seconds after his introduction following some super skill by Upson and Scott Malone created a half-chance.
The Lions kept up the pressure and McDonald was denied, this time after weaving past a couple of areas and despatching a low shot that lacked the power to cause Kuszczak any real problems.
Holloway's men kept their foot on the gas, but simply could not find a way through.
Jackson headed over and a piledriver from Garvan flashed no more than a foot over the bar in a frantic spell of Millwall pressure.
Keeper Forde even got involved, deep into injury-time, sprinting upfield to add another body in the box for a corner.
But there was to be no way back for Millwall, who stay just one point outside the bottom three with 13 games to go.
Forde, Fredericks, Malone, Shittu, Lowry (McDonald, 59mins), Williams, Upson, Garvan, Jackson (Feeney, 72mins), Easter (Morison, 58mins), Woolford. Subs not used: Bywater, Dunne, Beevers, Abdou.
Brighton & HA: Kuszczak, Saltor, Ward, Greer, Upson, Andrews, Stephens, Orlandi (March, 79mins), Ulloa, Lopez (Buckley, 58mins), Lingard (Forster-Caskey, 65mins). Subs not used: Dunk, Calderon, Rodriguez, Brezovan.
Scorer: Lopez (39mins, pen)
Ref: G Eltringham
Att: 12,149 (away 2,366)