Leyton Orient's Wembley dreams were shattered after a 90th minute goal from Ben Reeves sent them to a 3-2 defeat on aggregate at Southend United in the Johnstone's Paint Trophy area final.
Shaun Batt got the O's off to the ideal start when he netted his first goal for the club after just eight minutes. But the Shrimpers regained the upper hand when they levelled on the night through Barry Corr just after the hour mark.
Orient netted their second goal in the 72nd minute to level the tie at 2-2 when David Mooney headed home. But the O's were left stunned after Reeves' 90th minute goal fired Southend to Wembley.
Orient made two changes from the side beaten by Hartlepool at the weekend. Dean Cox returned to the side in place of the cup tied Charlie MacDonald. Gary Sawyer was ruled out with a knee injury and Leon McSweeney took his place.
The visitors made a bright start and had an early opportunity from Cox's free-kick but Lloyd James' shot was blocked by a defender.
The O's got off to a perfect start as they levelled the tie with an eighth minute opener. Cox received the ball from Moses Odubajo and the winger sent in a cross which was finished off neatly by Batt.
Orient nearly added a second shortly afterwards when Mooney curled a shot just past Paul Smith's post.
It was a dominant first 20 minutes for Orient who had controlled possession and got the all-important goal to cancel out Southend's first-leg lead.
Orient had another chance but Batt's shot from the edge of the area was straight at keeper Smith.
The League One side also came close from a Cox free-kick which was headed just over by Mooney.
Southend finally had their first attempt on goal on the half hour mark when Reeves' shot was comfortably saved by Jamie Jones.
Batt was heavily involved in Orient's attacks and the Millwall striker had another chance but drilled his effort wide of the post.
The Shrimpers started the second half with real purpose as they tried to lift the crowd. Reeves had a chance but blasted his effort well over the bar.
The O's thought they should have had a penalty when Cox went down in the area but referee Andy Woolmer waved play on.
Southend came close to getting off the mark when Ryan Leonard headed narrowly over the bar.
But the hosts were rewarded in the 61st minute with the equaliser which restored their slender lead in the tie. Kevan Hurst's free-kick was flicked on by Britt Assombalonga and substitute Corr volleyed the ball into the net.
It nearly got even worse for Orient shortly afterwards when Watford youngster Assombalonga headed narrowly over Jones' bar.
The O's responded and Batt fired in a shot from a tight angle which was saved by Smith's feet.
Orient grabbed their second goal of the night after 72 minutes to square the tie once more. McSweeney sent in a cross and Mooney rose to head home in front of the visiting supporters.
Mooney had the chance to score again minutes later but he tapped the ball into the side netting from close range.
The visitors came agonisingly close to grabbing the decisive goal ten minutes from time when Cox sent in a cross but Batt's effort cannoned off the bar to Southend's relief.
Orient were looking the more dangerous side in the closing stages and they had another chance through James but his long-range effort floated past the post.
Just as the match was heading to penalties, Orient were left shattered after Hurst's cross was neatly tucked home by Reeves to send Southend to Wembley.
There was not enough time for the O's to rescue the tie and it was a desperate late blow for them as the Southend fans celebrated with a mass pitch invasion at the final whistle.
Southend United: Smith; Clohessy, Barker, Prosser, Phillips; Hurst, Lund, Leonard, Reeves, Woodyard (Corr, 35); Assombalonga
Subs not used: Straker, Eastwood, Mayor, Bentley
Leyton Orient: Jones; McSweeney, Cuthbert, Baudry, Odubajo; Cox, Rowlands (Griffith, 74), James, Cook; Batt, Mooney
Subs not used: Vincelot, Smith, Clarke, Omozusi
Referee: Andy Woolmer