Southend moved into the automatic promotion places and plunged Hereford into the bottom two with an away win.
Shrimpers striker Neil Harris's second-minute shot was cleared by Kenny Lunt but referee Brendon Malone ruled it had crossed the line.
Strike partner Elliot Benyon scored from close range before Yoann Arquin's penalty for the Bulls.
Ryan Hall restored the two-goal lead from 30 yards before Nathan Elder's late close-range consolation.
VIEWS FROM THE DRESSING ROOM
Hereford manager Richard O'Kelly told BBC Hereford and Worcester:
"You're looking and you are thinking: 'Are they a bit tired; have we worked them too hard this week?'
"Then the tempo and the brightness suddenly kicked in and with 10 minutes to go with lifted it up a gear.
"I know it helps that you suddenly get a goal back but you are looking for a performance whether goals go in or they don't.
"You are looking for that from your players and that wasn't there today."