Gary Hart celebrated his 300th appearance for the club with the only goal two minutes into injury time.
Hart pounced from close range when the Millwall defence failed to deal with a cross by Leon Knight.
The Lions finished with ten men, defender Marcus Phillips receiving his marching orders for a second bookable offence three minutes into injury time.
The young defender had already been booked late on for a foul on Knight when he brought down Daniel Harding to become the third Millwall player dismissed in the last two matches.
It completed a miserable afternoon for Phillips. He wasted the visitors' best chance of a dour match when he headed over from close range in first-half injury time.
Dennis Wise's play-off chasers, depleted by injuries, suspensions and Scott Dobie's move to Nottingham Forest, have now not scored from open play for almost ten hours.
Phillips' chance apart, they rarely looked like changing that statistic.
Brighton rarely threatened as well in a game where defences were firmly on top.
Harding had one of the home team's best efforts in the fifth minute, exchanging passes with Guy Butters before firing just wide.
Brighton's former Millwall striker Mark McCammon failed to make much of an impact against his old club.
McCammon, booked along with Millwall's Marvin Elliott for a first-half wrestling match, was substituted with a back injury in the second half.