Darren Byfield's goal midway through the first half condemned the home side to a sixth defeat in succession in all competitions.
Millwall are now only a point behind them towards the foot of the table and they have a game in hand.
Brighton boss Dean Wilkins and striker Alex Revell both missed the match through illness, and they will not be feeling any better after Byfield was gifted his eighth goal of the season in the 22nd minute.
A hopeful long ball out of defence by Millwall captain Paul Robinson cleared the head of Joel Lynch to leave Byfield in the clear. Keeper Wayne Henderson hesitated before coming off his line and was beaten by a clinical lob.
Brighton pressed for an equaliser for the rest of the first half but their attacking efforts lacked conviction.
Adam El-Abd somehow managed to drag a shot wide from a tight angle out for a throw in when well placed from a pass by Joe Gatting.
Dean Cox wasted another chance, finding only the side netting after Danny Senda miss-controlled the ball inside his own box.
Brighton continued to dominate possession after the break, but they struggled to carve out opportunities against a resolute Millwall defence.
Jake Robinson went close with a well struck effort from 35 yards which whistled narrowly wide of the target.
Assistant manager Dean White and coach Ian Chapman, taking charge of the Brighton team in Wilkins' absence, made a double substitution with 17 minutes left.
Nathan Elder, signed from Billericay, came on for his debut at the expense of Gatting and youngster Tommy Fraser took over from the experienced Richard Carpenter in midfield.
The changes almost paid off as the powerful Elder met a teasing cross from Fraser with a downward header which forced Millwall keeper Lenny Pidgeley into a scrambling save at the foot of the post.