Dagenham suffered their sixth defeat of the season after two highly debateable decisions on the stroke of half time completely altered the complexion of this explosive encounter.
First Barry Jones' header from a corner was cleared by Steve Potts on the line but the referee called the play back.
Southport appealed for a goal but referee Martin Yearby belatedly awarded a penalty and sent off Potts.
Steve Soley sent Tony Roberts the wrong way to make to 1-0.
Moments later Daggers' hopes of a revival were extinguished when once again Jones was involved. This time he went down holding his face and Yearby sent off Mark Stein for an apparent use of the elbow.
The crowd erupted in fury as did chairman, management and playing staff.
Yearby was escorted back to the dressing room at half time.
Before the pivotal incident Daggers had looked slightly the better side.
Danny Hill was excellent in his creative role, while Southport were content to contain and defended very well.
Daggers' best moment was when Stein saw his tenth minute effort cleared off the line by Martin Clark.
But the second half offered them nothing but tired legs in the end despite their tremendous efforts.
Danny Shipp had the best moment when his shot was saved by Steve Dickinson when he could have done better.
Southport defended professionally, and Soley flicked them further in front with his heal before Peter Thomson powered clear to smash home the third.
They could have added more but it would have heaped further injustice on the Daggers whose angry manager Garry Hill promised that they will study video evidence and make an appeal