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.
They 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.
The penalty was awarded against Yeovil left-back Nathan Jones for bringing down Lee Barnard and Barnard got up to slot home the spot-kick himself. He beat home keeper Asmir Begovic low to his left hand.
Both teams had chances in the second half but Yeovil lacked a cutting edge and were thwarted on occasions by good saves from Adam Federici, the Shrimpers second-choice keeper who stepped in for the injured Steve Mildenhall.
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.
In addition to losing Schofield and Roberts who now face bans, Yeovil's small squad is currently decimated by injuries.
Fortunately, they now have a fortnight's rest as their scheduled fixture at Leicester next Saturday has been postponed as City have international calls.