Darren Byfield's first-half goal gave Millwall victory and condemned Brighton to a sixth successive defeat.
Byfield stole on to captain Paul Robinson's long ball to lob keeper Wayne Henderson after 21 minutes.
Seagulls' boss Dean Wilkins was unable to attend the game because he was suffering from flu.
Brighton had chances after the break, with Jake Robinson only inches away, but Millwall defended well for their first away clean sheet this term.
Brighton: Henderson, O'Cearuill, Lynch, Butters, Rents, Hart (Frutos 78), Carpenter (Fraser 73), El-Abd, Cox, Robinson, Gatting (Elder 74).
Subs Not Used: Kuipers, Elphick.
Booked: Cox.
Millwall: Pidgeley, Senda, Robinson, Shaw, Craig, Hackett (Zebroski 67), Ardley, Elliott, Dunne, Harris, Byfield (May 83).
Subs Not Used: Day, Hubertz, Williams.
Booked: Shaw, Dunne, Byfield, Elliott.
Goals: Byfield 22.
Att: 6,226
Ref: M Russell (Hertfordshire).