Substitute Ronan Murray headed Swindon Town into the southern area final of the Johnstone's Paint Trophy.
After Matt Ritchie's corner was put back into the box by Lander Gabilondo, Ipswich loan man Murray scored just two minutes after coming on.
Southend led when Sean Clohessy's diagonal ball from the right was bundled down by Luke Prosser for Blair Sturrock to prod in from six yards.
But Swindon levelled when Paul Caddis curled home from just outside the box.
League Two leaders Southend, unbeaten in 17 games since losing to Swindon at the County Ground in early September, were hoping to set a new a club record. But, instead, it was Paolo di Canio's Robins who stretched their own run to 13 matches without defeat.
After knocking Southend's local rivals Colchester out of the FA Cup on Saturday, victory completed a fine four days in Essex for Swindon, who will now tackle Barnet in the area final.
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Southend manager Paul Sturrock told BBC Essex:
"We're obviously disappointed, going one-nothing up, we looked a bit complacent, I thought we dropped off the pace a wee bit and we've paid dear for it.
"It's been a fantastic run, we've got to start a new run now, its up to the players to respond properly.
"We've got a big game coming up on Saturday, the players will have to get their heads up."
Swindon Town manager Paolo di Canio told BBC Wiltshire:
"We came out and scored two goals and we should have scored another two. We deserved this victory and it is crucial.
"Before, I used to say 'we need to keep both feet on the ground' but now I know my team do as they are intelligent.
"But I've told them enough celebration. From tomorrow we are thinking about the league."