Ben Reeves scored a 90th minute equaliser to send Blues to Wembley after a 3-2 aggregate win against Leyton Orient in the Johnstone's Paint Trophy.
Shaun Batt gave the away side the best start possible after eight minutes before substitute Barry Corr drew level.
A David Mooney header in the second half looked to take the game to penalties before Reeves popped up at the death to send Southend to Wembley.
Orient had the perfect start in the 8th minute with Batt giving the away side the lead, levelling the tie on aggregate.
Dean Cox’s low cross found Batt and the striker stole a yard on Mark Phillips before steering the ball past Paul Smith in the Blues goal.
Mooney then tried his luck minutes later after finding space 25 yards but his curling effort was way off target, giving Smith no trouble at all.
Mooney came even closer in the 25th minute after he directed Cox’s free kick towards goal with a looping header which narrowly missed the target, landing on the roof of the net.
The home side tested Jamie Jones in the 30th minute after Britt Assombalonga turned Scott Cuthbert before playing Ben Reeves who fired a low left footed strike at goal which the keeper claimed.
With half time approaching Mathieu Baudry’s last ditch header prevented substitute Corr from getting on the end of Reeves’ dangerous cross as Blues looked to equalise in the match.
Both teams came out attacking in the second half with Cox running in on goal after excellent team play before Matthew Lund made a last ditch tackle.
Southend hit back in the 59th minute after Reeves’ deep cross found Ryan Leonard at the back post who headed over the bar from a tight angle.
The home side found the equaliser and took the lead on aggregate through Corr’s clinical effort from 12 yards.
Hurst’s free kick was nodded down by Assombalonga as he out jumped the Orient defence and the ball fell kindly to Corr who expertly volleyed home off the underside of the bar sending the Roots Hall faithful into raptures.
Orient nearly went ahead through Batt again in the 67th minute after he superbly turned Luke Prosser on the line before trying to sneak an effort in at the front post which Smith was equal to saving with his legs.
The away side found the breakthrough in the 72nd minute through Mooney’s header after the striker connected well to Leon McSweeney’s cross.
The goal brought the scores level on aggregate after Mooney’s powerful header flew past Smith in the Blues goal.
Orient nearly scored again on the counter attack after Cox broke free down the right and sent an inviting ball into the box which was met by Batt only for the ball to hit the top of the crossbar with Smith stranded.
With 90 minutes on the clock Southend found the equaliser through Reeves giving Blues the advantage in their quest to Wembley.
Hurst done superbly on the wing to find the cross which Reeves slotted in excellently with his left foot leaving Jones rooted.