Armand Gnanduillet was the match winner as Blackpool earned an invaluable three points on the road to elevate them to the cusp of the League One play-offs.
The striker scored seven minutes from time to earn the win after the Seasiders had been pegged back just eight minutes earlier.
It came after Ollie Turton had given Blackpool the lead just 14 minutes into the first half.
The home side ended the game with 10 men after Michael Turner was shown a straight red just five minutes from time.
The win means Blackpool, who have now four games on the bounce, are seventh in League One, level on points with Charlton Athletic who occupy the final play-off spot.
It was Pool's first win at Roots Hall since 2001.
Blackpool were back to full strength for today’s clash, with Terry McPhillips opting to make six changes from last weekend’s 3-2 FA Cup first round win at Exeter City.
Mark Howard returned in goal after a four-game absence through a thigh injury, seeing Christoffer Mafoumbi drop out of the squad.
Marc Bola and Jay Spearing also returned after missing the last two cup games.
Having scored three goals in those two cup clashes against Exeter and Accrington Stanley respectively, Joe Dodoo was handed his first league start since September.
Armand Gnanduillet also kept his spot in the side having scored in Tuesday night's Checkatrade Trophy win.
Jordan Thompson missed out due to his international commitments with Northern Ireland, while Ryan McLaughlin, Joe Bunney and Paudie O'Connor were the three left out of the squad.
Despite some mixed recent form in League One, the Shrimpers made a strong start to the game and came within a whisker of taking the lead inside seven minutes.
It followed a defensive mix up between Howard and Ben Heneghan, leaving the Blackpool goal wide open. Former Premier League winger Michael Kightly lobbed an audacious effort over Howard but it hit the inside of the post, before Pool managed to clear their lines.
The Seasiders managed to hit back in the perfect fashion as they took the lead on 14 minutes.
It was a simple but effective goal too, as Marc Bola delivered a low cross from the left for Ollie Turton, finding himself in the unusual position in the six-yard box, who tapped home from close range for his first goal of the season.
Southend looked for an immediate response, Stephen Hendrie dragging a shot wide of Howard’s goal after space had opened up for the hosts in the final third.
Chris Powell’s men against came close with Simon Cox getting across his man before glancing a header wide of the far post.
Howard then got down well to save Sam Mantom’s low strike from 25 yards.
The effectiveness of Blackpool’s first-half performance was demonstrated by the subdued atmosphere at Roots Hall, which wasn’t at all helped by the home side continuing to lose possession.
The Seasiders almost made the perfect start to the second half, when on 51 minutes Jay Spearing rattled the woodwork.
It was a superb 25-yard effort from the returning midfielder, which took a slight deflection before hitting the underside of the Southend crossbar.
The following chance, which fell the way of Gnanduillet, came in an entirely different fashion as the striker looked to stretch and reach Mark Howard’s free kick, which was pumped straight into the Southend box. Unfortunately for the Seasiders the striker couldn’t get the required contact to divert towards goal.
At the other end, the home side had penalty appeals waved away as substitute Shawn McCoulsky went down under the challenge of Tilt.
Southend began to build up a little pressure, with Howard forced to produce a smart stop to tip over Hendrie’s rising volley.
Further penalty appeals were then waved away for the hosts, with Cox the man to go down in the box on this occasion.
Blackpool were agonisingly close to doubling their lead with another long-range effort from Spearing, who saw his left-footed shot whistle agonisingly wide of the upright.
Just two minutes later, the Seasiders were pegged back with just 15 minutes to go as Jason Demetriou levelled for the home side.
It came in similar circumstances to Blackpool’s goal, with Timothee Dieng lofting a cross to the back post where Jason Demetriou steered home from close range.
But eight minutes later, Pool were back in front. It came via Gnanduillet, bagging his second in as many games, heading into the bottom corner after being set up by substitute Harry Pritchard.
It went from bad to worse for Southend, who were reduced to 10 men with just five minutes to play when defender Michael Turner was shown a straight red, the referee signalling for a stamp.
The Seasiders had chances to make it more comfortable in the dying stages of the game, but in the end it didn’t matter as Terry McPhillips’ men held on for the three points.
Southend: Oxley, Demetriou, Turner, Moore, Hendrie (Robinson), Bunn, Dieng, Mantom, Kightly (McLaughlin), Yearwood (McCoulsky, Cox
Subs not used: Bishop, Bwomono, Kyprianou, Hyam
Blackpool: Howard, Turton, Daniels, Tilt, Heneghan, Bola, Spearing, Guy (Pritchard), Delfouneso, Dodoo (Nottingham), Gnanduillet
Subs not used: Boney, Taylor, O’Sullivan, Feeney, Cullen
Referee: Nick Kinseley
Attendance: 6,882 (241 Blackpool)