James Brown's two goals early in the second half gave the home team a 3-1 lead, but three goals in the last eight minutes made it closer than it looked as if it was going to be.
In an end-to-end first half, both teams scored from the spot.
Hartlepool had first go with Richard Barker hammering his 12th goal of the season after Brown was tripped just inside the area by Adam Barrett.
Hartlepool dominated for a spell after the goal with Michael Nelson flicking a near-post header inches wide after a right-wing free-kick from Alan Thompson and Matty Robson going just as close with a low shot from the left that flashed across goal and wide of the far post.
But Southend were level on the half-hour when Steve Hammell blasted his spot-kick into the roof of the net after Nelson was judged to have fouled Mark Gower near the penalty spot.
Brown struck his first on 47 minutes after chesting down a chip into the area by Richie Humphreys before slotting his low shot in from 15 yards.
On 52 minutes he was there again to volley in from the same spot after Richard Barker's shot was blocked and the ball spun into the air.
Eight minutes from time Gower was unmarked to tap in and narrow the gap, but substitute Anthony Sweeney slammed in the home team's fourth after being set up by Joel Porter.
Southend still refused to be beaten and Tommy Black volleyed in to make it 4-3, but Hartlepool just hung on with some desperate defending.