Yeovil Town had two players sent off in stoppage time as they slipped to their first home defeat of the season but Blues to their fourth successive win and seventh place in the table.
Danny Schofield was straight red-carded by referee Keith Hill for a foul and when Gary Roberts protested he was shown a second yellow card for dissent.
Southend went into the match without recent signing Dougie Freedman who was injured but they played well enough to keep their winning run going.
Dougie being missed for the way he can hold the ball up, especially in the appalling conditions, something his replacement Alex Revell seemed unable to do.
Blues took the lead in the 24th minute from a penalty and for a long time it looked as though that might win the game. But in the final four minutes of the match both sides found the net again with Yeovil going further behind before they managed a consolation goal.
With the wind behind them the home side got the ball in promising attacking conditions several times but only Tomlin seemed to really trouble the Southend defence, forcing a brilliant Federici save low down when it seemed certain he would open the scoring.
In the end that fell to Southend. The penalty being awarded against Yeovil left-back, and less than popular ex Blue Nathan Jones, for bringing down Lee Barnard, and the good Lord got up to slot home the spot-kick himself.
Barny beat home keeper Asmir Begovic low to his left hand while earning shouts of cheat from the home crowd for his troubles, looked a good call from the other end.......though the distance and rain made my opinion less than reliable!
Towards the end of the first 45 the ref went on to turn down a clearer shout for another Southend spot kick, then in added time Yeovil missed two clear chances in as many seconds to equalise as the ball flashed across the six yard box.
Both teams had chances in the second half but Yeovil continued to lack a cutting edge and were thwarted on occasions by more good work from on-loan Aussie Adam Federici, in for the injured ex-Glover Steve Mildenhall.
After all the talk of not being complacent there was a feeling that Southend were being just that, being outplayed for long periods of the second half when many felt it would be the other way with the wind in the Shrimpers favour.
Captain Adam though battled throughout as the wind and rain made the game tougher for both sides and thoroughly deserves man of the match.
In the 86th minute Southend increased their lead when Simon Francis picked out Hal Robson-Kanu who curled a superb left-footed shot past Begovic.
Almost immediately Yeovil pulled a goal back. Substitute Andre McCollin produced some good work on the left and his pass was touched in from close range by Schofield.
Then the fun started as Blues played out time in the corner Scofield went in with a mindless two footed tackle on HRK and quite frankly Mr. Hill had no other choice. It did mean six minutes of injury time was added on but the points were ours.
The ref then waited until a police escort arrived to march him and his team off the pitch to the baying Yeovil home crowd. However that's not Southends' problem as they marched on to a place one point outside the play-off zone.
A full 'Day Tripper' and 'Marks out of 10' tomorrow when I finally dry out but it makes next weeks clash with Stockport, three places and two points behind Blues, a very tasty prospect indeed.