Albion slumped to their fifth straight defeat and finished with ten men for the second match running.
Robbie Pethick was sent off shortly after Darren Ward nodded Millwall's 73rd minute winner.
The rightback received a straight red card following an incident off the ball with Belgian substitute Christophe Kinet.
Loan signing Graham Barrett received his marching orders on his debut at Portsmouth last week and Pethick's dismissal means more disciplinary trouble for Martin Hinshelwood's strugglers.
Pethick also now faces an automatic three-match ban from September 21.
A workmanlike, backs to the wall display by the Seagulls looked like stopping the rot until Ward's soft decider.
The centre half back headed Kinet's corner into the net from inside the six yard box to earn the Lions their second successive home victory.
Guy Butters, who performed solidly on his second appearance for Albion, chastised goalkeeper Andy Petterson. He felt the Australian should have dealt with the situation.
Albion could have no complaints about the outcome. They battled hard in front of a crowd of 8,822 at The New Den, but Millwall had most of the match and the chances.
The Seagulls had their best spell in the middle of the first half, when Paul Kitson volleyed just wide on his comeback from a back related hamstring injury.
Kitson was at the centre of controversy in a stormy second half.
The former West Ham marksman was booked for a late challenge on Burgess Hill-based defender Matt Lawrence a minute after he had himself been fouled from behind by Stuart Nethercott, which earned the Millwall captain a caution as well.
Albion will be desperate to end their miserable run against Third Division Exeter in the Worthington Cup at Withdean on Wednesday.
Comments: Our rules
We want our comments to be a lively and valuable part of our community - a place where readers can debate and engage with the most important local issues. The ability to comment on our stories is a privilege, not a right, however, and that privilege may be withdrawn if it is abused or misused.
Please report any comments that break our rules.
Read the rules hereComments are closed on this article