Andy Barcham put the seal on a 3-0 win which propelled Gillingham towards safety and left Southend deep in trouble.
Dennis Oli put the Gills ahead on 47 minutes, Renee Howe drilled the second and Barcham wrapped it up as the Shrimpers slumped to their eighth straight away defeat.
United posed their biggest threat from set-pieces and nearly profited when Simon Francis' eight-yard strike forced a sharp reaction save from goalkeeper Alan Julian.
Howe was guilty of missing a golden opportunity to put Gillingham ahead at the break as he slammed a six-yard shot straight at Southend stopper Steve Mildenhall.
But Gillingham went ahead 69 seconds after the restart when Curtis Weston cleverly beat defender Pat Baldwin and, after his effort was blocked, Oli hooked in the rebound.
Substitute Simeon Jackson teed up Howe to double the lead after 74 minutes and Barcham settled the encounter five minutes from the end.
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