Manager Simon Grayson rested six players for the newly-promoted Championship side and almost paid for it as Southend, who knocked out Manchester United to reach last season's quarter-finals, looked set for another fourth-round appearance following Matt Harrold's sixth-minute penalty.
But Blackpool striker Scott Vernon struck an 81st-minute equaliser to spare the Championship side's blushes and take the game into extra-time.
• Jackson's prediction comes through
Defender Jackson was then belatedly brought into the fray and with a penalty shoot-out looming, stabbed home the winner three minutes from time.
Southend, who swapped places with Blackpool last season, came into the game with high spirits after winning their last three League One matches and made just one change, with striker Charlie MacDonald coming in for the cup-tied Leon Clarke.
And MacDonald made his presence felt after just six minutes, winning the penalty from which Southend opened the scoring.
Tommy Black played a neat ball through for the summer signing from Ebbsfleet, who was brought down by goalkeeper Rhys Evans, and Harrold stepped up to hit the spot-kick straight down the middle.
Southend full-back Adam Barrett denied Blackpool a quick equaliser and saved Peter Clarke's blushes with a goal-line clearance after the ball deflected goalwards off the former Tangerines defender.
Blackpool took time to find their feet but began to gain control midway through the half.
The impressive Andy Welsh exchanged passes with Vernon to get to the byline in the 27th minute, although Keigan Parker somehow managed to sidefoot his cross over from six yards.
Parker then picked out Welsh at the far post a minute later and the former Sunderland winger's volley rolled agonisingly wide.
Blackpool failed to keep the pressure on heading into the break but showed greater urgency following the restart.
Welsh had a strong penalty appeal turned down for a nudge by Garry Richards, but again Blackpool failed to maintain their momentum.
Grayson threw on midfielder Wes Hoolahan and striker Andy Morrell on the hour mark in a bid to revive his side but Southend comfortably held firm and threatened themselves in the 75th minute when Nicky Bailey's curling effort was deflected over.
But that narrow escape roused Blackpool with David Fox dragging a 20-yard effort narrowly wide before a superb run by substitute Hoolahan finally unlocked the Southend defence.
Hoolahan left Lewis Hunt on the floor, and although his shot was blocked by a covering defender on the line, Welsh squared for Vernon to sidefoot home and take the game into extra-time.
Welsh's probing runs continued to cause Southend problems in extra-time and drew a tired foul from Harrold in the 104th minute, with Welsh forcing a decent save from Steve Collis with the resulting free-kick.
Substitute Jackson looked to have put Blackpool in front a minute after the restart when he met a Welsh cross but the Seasiders skipper glanced his diving header across goal.
However, the veteran defender made no mistake in the 117th minute, stabbing home at the back post after Southend failed to clear Welsh's corner.
Jackson's prediction comes throughBlackpool manager Simon Grayson revealed Michael Jackson predicted his goal
that sealed tonight's 2-1 victory over Southend and sent the Seasiders into the
last 16 of the Carling Cup.
Jackson came off the bench to stab home a late extra-time winner to take the
Tangerines into the fourth round for the first time in 34 years.
The Blackpool captain scored the penalty that sealed a shoot-out victory over
Barclays Premier League Derby in the previous round - and despite starting on
the bench against Southend, Jackson sensed he would again be Blackpool's Carling
Cup hero.
'He said before the game he'd get the winning goal,' said Grayson. 'He thought it'd be a penalty - but full credit to him for being in the right
place at the right time. Most of his goals come from his head, and he finished
it well.'
Jackson was one of eight changes from Saturday's starting line-up, with six of
those players rested, and Grayson was almost made to pay.
Southend, who knocked out Manchester United to reach last season's
quarter-finals, looked set for another fourth-round appearance as the Coca-Cola
League One side led for much of the match through Matt Harrold's sixth-minute
penalty.
But Blackpool striker Scott Vernon struck an 80th-minute equaliser to take the
game into extra-time, and Jackson was brought into the fray in the 94th minute -
before claiming the winner.
'We went a little unorthodox with three at the back, and it led to the
equaliser,' said Grayson. 'After we got the goal, I could see us winning the game playing 4-4-2 - so it
was important that `Jacko' came on, and the captain came good again.'
Blackpool's late rescue act made it six matches unbeaten for the
newly-promoted Coca-Cola Championship club.
'The lads never know when they're beaten,' added Grayson. 'First half was stop-start for us, which can be expected with the changes we
made. In hindsight, you don't want to make too many changes - but we had to,
through injuries and the run of games that we had.
'But the players dug in there. Second half, we created some chances and we're
thinking maybe it won't happen for us. But we got the late goal, and in
extra-time I thought we looked like the team that was going to win it.'
Southend boss Steve Tilson felt his team coped well with Blackpool until the
hosts finally made the breakthrough as the Shrimpers tired.
They now face league games at Port Vale and Bristol Rovers over the coming
week, and Tilson is concerned how his players will react.
'We knew it was going to be a tough game, and it's disappointing to come so
close and get so far,' he said.
'I thought second half we looked more comfortable than in the first half; I
didn't think they had that many chances.
'It's disappointing to concede two goals late in the 90 minutes and then
extra-time. Now we've got a massive game on Saturday, and that's going to take a
lot of them. They've worked hard tonight.'
Blackpool 2 - 1 Southend United 
