They appeared to be coasting to victory before three goals in the last eight minutes threatened to turn the game on its head.
Both teams were on target with well-taken penalties in the first half. Richard Barker struck first, blasting his 12th of the season after James Brown was felled just inside the area by Adam Barrett.
Michael Nelson headed just wide and Matty Robson came close as Hartlepool dominated for a spell. But Southend hit back with a spot-kick of their own on the half hour, Steve Hammell following Barker's example and hammering his shot in after Nelson's foul on Mark Gower.
Two Brown goals in six minutes early in the second half gave Hartlepool control. His first came after 47 minutes when he chested down a Ritchie Humphreys cross and drilled a low shot home from 15 yards. And he was in the same place after 53 minutes when Barker's shot was blocked, pouncing to volley in the rebound.
But Southend narrowed the gap in the 82nd minute when Gower tapped in, only for home substitute Antony Sweeney to make it 4-2 after 89 minutes from Joel Porter's pass. Tommy Black finished the scoring in the last minute as the whistle came to Hartlepool's rescue.
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