Southend never recovered after conceding an early goal, and had to work hard with ten men in the last half-hour after skipper Adam Barrett was sent off.
Pools went ahead on four minutes with a well-worked strike. Joel Porter, back in the side after injury, got away wide on the right and after cutting inside he pulled a great ball back from the by-line into the path of Kevin Kyle, who curled his 15-yard shot into the top corner of the net.
And three minutes later it was almost two when Matty Robson got away on the left, but his angled shot brought a great one-handed save from keeper Steve Mildenhall.
But after Lee Barnard blasted a good Southend chance over an open goal on 18 minutes, Hartlepool made it two ten minutes before the break.
A poor clearance landed at Robson's feet on the left and with nobody challenging he moved forward before curling a brilliant 30-yard shot into the far top corner of the net.
Twelve minutes into the second half, it got worse for Southend when skipper Barrett, booked in the first half, was shown a straight red card for a last-man challenge on Porter.
And the ten men were punished four minutes later when Kyle tapped in his second after Robson brought down a right-wing cross from Richie Jones.
Down to ten men and well behind, Southend had to work hard to keep the score down, though Gary Liddle twice went close with low long-range shots as Hartlepool pressed forward almost non-stop in the last half-hour.