Hartlepool survived a frenetic finish to grab their first win in seven games. Richard Barker put Pools ahead with a penalty after Adam Barrett fouled James Brown before Steve Hammell scored from the spot after a foul on Mark Gower.
Brown scored twice, from a Richie Humphreys cross and then a volley, before Southend's Gower tapped in from close range with eight minutes left.
Antony Sweeney converted Joel Porter's pass to make it 4-2 but there was still time for Tommy Black to volley home.
Hartlepool: Lee-Barrett, McCunnie, Nelson, Antwi , Humphreys, Brown, Liddle, Thompson (Sweeney 70), Robson, Porter, Barker.
Subs Not Used: Budtz, Elliott, Foley, Mackay.
Booked: Nelson, McCunnie.
Goals: Barker 17 pen, Brown 47, 53, Sweeney 90.
Southend: Flahavan, Francis, Clarke, Barrett, Hammell, Hunt, McCormack, Bailey, Gower, Black, Hooper (Scannel 77).
Subs Not Used: Collis, Maher, Richards, Moussa.
Booked: McCormack, Hunt.
Goals: Hammell 30 pen, Gower 83, Black 90.
Att: 3,217
Ref: Carl Boyeson (E Yorkshire).
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