Blackpool manager Simon Grayson's gamble of making six changes from the side which has been operating comfortably in the Championship almost played right into Southend's hands.
The Seasiders had been plagued with some goalkeeping errors in recent games and Grayson brought in Rhys Evans so he could stake a claim.
However, the match was just six minutes old when Evans badly timed lunge at Charlie MacDonald's legs saw Southend awarded a penalty which Matt Harrold converted.
It was just the start Southend had hoped for as their keeper Steven Collis hardly had to make a save courtesy of his dominant back four.
When Blackpool did get chances they spurned them with the worst culprit being Keigan Parker, who missed one from just two yards out which could hardly have impressed the scouts watching the want-away striker.
It took the arrival of Blackpool's Irish talisman Wes Hoolahan to change the course of the game.
His darting run into the box in the 80th minute ended with two blocked shots before Scott Vernon forced the ball home from a narrow angle.
The game moved into extra-time with Collis earning his wages at last with two great stops from Andy Morrell and Jackson.
Jackson was causing problems at all the set pieces and, when Southend failed to clear a Hoolahan corner, the experienced defender slammed the ball in at the far post for the latest of late winners.