Simon Cox's sixth goal of the campaign was not enough to secure a point for Swindon at Roots Hall with Mark Gower's injury-time strike earning all the points for Steve Tilson's men.
The Reading loanee had pounced after just two minutes to fire his side in front, with Adam Barrett's 30th minute strike drawing level. However, Gower's last minute effort was a cruel blow with Swindon deserving at least a point for their hard work.
The Town management had made three changes to their starting line-up at Roots Hall with Chris Allen and Kaid Mohamed both making their full league debuts for the Robins.
Allen joined Easton and Pook in a midfield three with Cox and Mohamed both supporting lone striker Blair Sturrock. Mauro Almeida was included amongst the substitutes with Paynter and McGovern also named on the bench.
Town made a fantastic start to the game with Simon Cox netting after just two minutes. After kicking off Swindon made a solid start with some early pressure forcing the home side back. A shot 20-yard shot from Andy Nicholas was only parried by home keeper Collis, with Cox in the right place at the right time to fire home from close range.
The lead could have been doubled just five minutes later after a fantastic break from the visitors. Simon Cox's precise ball down the right found Sturrock in space and he took the ball on before unselfishly laying the ball into Pook's path. His shot was deflected just wide with the corner cleared. Cox then tried his luck from 35-yards with Town eager to make the most of their early pressure.
Southend's first real venture forward came with ten minutes on the clock - and it could have been a costly for Town. A long ball forward down the right was latched onto by Clarke and with the Town defence standing off, Clarke smashed a right foot angled shot from 20 yards which cannoned off the top of the crossbar.
The Shrimpers then continued in an attacking mood with Dean Morgan seeing his right foot snapshot fire high and wide after good build-up by strike partner Clarke. Mark Gower then found the safe hands of Brezovan with a low drive before Steve Hammell's free-kick was well held by the Town keeper on 23 minutes.
Swindon had another excellent chance to extend their lead on the half-hour mark. Kaid Mohamed had found space inside the box but tried to beat the extra man and the chance was gone with cover soon arriving for The Blues.
Hasney Aljofree was booked on 31 minutes after hauling down Clarke on the right hand edge of the area and from the resulting free-kick, Southend drew level. A free-kick Hammell was swung in and Adam Barrett rose highest to head his sixth goal of the season.
Immediately after the restart Leon Clarke raced clear and with Blackburn racing back, the former Wolves man fired a low shot just wide of the far post with Brezovan doing well to narrow the angle.
Half-Time: Southend United 1 Swindon Town 1
The home side won the first corner of the half on 48 minutes with a combination of Allen and Nicholas able to clear.
In return Swindon went on the attack and had a penalty appeal turned down. A corner from Allen resulted in a melee inside the box with Blackburn and Mohamed both trying their luck. A shot from Mohamed seemed to strike the hand of Barrett but the referee allowed the game to continue. Soon after Barrett was forced off after sustaining a first half injury with Garry Richards coming on in his place.
Swindon had frustrated the hosts inside the opening quarter of an hour of the second half with Aljofree and Blackburn combining well in the heart of the defence. Aljofree's bravery was once again in evidence on the hour with the Town skipper diving in to prevent a chance for Clarke on the edge of the six-yard box.
Caretaker bosses Byrne and Williams made their first chance of the afternoon on 62 minutes with former Southend man Billy Paynter handed an opportunity, replacing Sturrock as the lone striker.
Michael Pook almost put Swindon ahead with a 70th minute pile-driver. A neat knockdown from Paynter found the former Robins youth teamer and he saw his 25-yard drive fly narrowly over.
The home side had a chance of their own on 75 minutes with loanee Leon Clarke racing away from the Robins defence after a through ball. Clarke sprinted away towards the box and with only Smith and Blackburn back, Clarke squared the ball for Gower who was just unable to get the telling touch.
Dean Morgan was then replaced by Charlie McDonald for the home side on 76 minutes before J-P McGovern was introduced in place of Kaid Mohamed on the left of a front three. Mohamed had enjoyed a positive first league start with his efforts recognised by the 373 travelling Town fans.
As the rain continued to fall at Roots Hall Swindon continued to venture forward in search of the crucial second goal. Strikes from Nicholas and Pook did come inside the 83rd minute with the game flowing from end to end.
Miguel Comminges replaced Simon Cox on the right hand side as injury-time approached with the home side making the most of the three minutes added to the game. Mark Gower poubced inside the box with a neat finish to seal all the points for The Blues.
Full-time: Southend United 2 Swindon Town 1
Southend Scorers: Barrett '31, Gower '93 + 1
Swindon Scorer: Cox '2
Attendance: 7,403 (373 from Swindon)
Swindon Town: Peter Brezovan; Jack Smith, Chris Blackburn, Hasney Aljofree ©, Andy Nicholas; Michael Pook, Chris Allen, Craig Easton; Simon Cox, Blair Sturrock, Kaid Mohamed
Substitutes: Mark Scott (GK), Jon-Paul McGovern, Miguel Comminges, Billy Paynter, Mauro Almeida
Southend United: Steve Collis; Lewis Hunt, Peter Clarke, Adam Barrett, Mark Gower, Kevin Maher (c), Dean Morgan, Alan McCormack, Steven Hammell, Nicky Bailey, Leon Clarke
Substitutes: Darryl Flahavan, Charlie McDonald, Garry Richards, Gary Hooper, Franc Moussa
