The visitors took the lead after eight minutes when Adam Boyd fired low beyond a diving Steve Mildenhall.
Chris Turner’s men doubled their advantage after 31 minutes when Andy Monkhouse’s effort from 25 yards took a big deflection off Anthony Grant and flew beyond Mildenhall, with the latter accredited with the own goal.
Then, after Steve Tilson’s half-time teamtalk, Francis Laurent pulled one back for the Shrimpers in the 49th minute when he got on the end of Scott Malone’s free-kick to head home via the right-hand post.
The Blues got on level terms in the 56th minute when Alan McCormack found an unmarked Lee Barnard who slid the ball home from six yards.
Barnard then put Southend in front on 75 minutes when he nodded home Damian Scannell’s cross from six yards for his 16th goal of the season. Hartlepool’s misery was compounded five minutes from time when substitute Ben Clark was shown a second yellow card for felling McCormack.