A second-leg draw was good enough to send Crewe into the League Two play-off final at Southend's expense.
Leading 1-0 from the first tie, the Alex doubled their aggregate lead with AJ Leitch-Smith's fine finish.
Neil Harris pulled one back following Steve Phillips's fumble before Max Clayton once again extended the visitors' advantage.
In a frantic finish Chris Barker nodded home Ryan Hall's cross but it was not enough to stop Crewe reaching Wembley.
It was a true display of the lottery of the play-offs as Southend, who spent a large part of the season top of the league only to narrowly miss out on automatic promotion, were put to the sword by a Crewe side who were 12th when the two teams met in February .
That loss triggered a remarkable undefeated run for the Alex, who have now gone a club-record 18 games without tasting defeat.
Did you know?
Crewe top scorer Nick Powell, who set up his side's second goal, has been scouted this season by Manchester United, Arsenal and Chelsea
And they took the lead at Roots Hall when Ashley Westwood won a battle with Anthony Grant in the centre of the park before releasing Leitch-Smith down the left. He showed the quickest of feet to cut into the area and send an arching drive beyond Belford.
Southend thought they had pulled one back when Freddy Eastwood snaffled the chance after Phillips had parried Hall's strike, but the Coventry loanee had roamed offside.
Crewe, exploiting the space as Southend continued to push forward, were handed plenty of chances to put the tie to bed.
Belford's mis-kicked clearance fell into Byron Moore's path, but he blazed over with only the keeper to beat and Leitch-Smith, who moments earlier had been harshly booked for diving, hit his effort tamely at the keeper when Lee Bell had chipped him through.
Finally the Southend fightback came and Crewe had both posts to thank for preserving their lead as Michael Timlin struck one and then Eastwood the other.
The breakthrough arrived moments later, with Phillips failing to collect Barker's cross and substitute Harris sweeping in the loose ball.
The joy was short-lived though, as Crewe's highly fancied youngsters Nick Powell and Clayton combined, the latter finding enough space under pressure to fashion a cute finish, which sneaked just inside the wrong-footed Belford's left upright.
Barker hit back late on, applying the finish to Hall's stunning chipped cross, but it was not enough to stop Steve Davis's men from continuing their march towards Wembley, where they meet either Cheltenham or Torquay.
VIEWS FROM THE DRESSING ROOM
Southend manager Paul Sturrock told BBC Essex:
"You can't play a game like we've tried to play, 45 minutes of football. If we'd shown that aggression and appetite in the first half, I think we'd have come out the victors.
"The biggest game of the season and we just didn't get to grips with the game at all. They were the eager team and got the goal they deserved.
"I think we shaded the second half, but the horse had bolted by then. I'm absolutely gutted for everybody involved with the football club."
Crewe Alexandra manager Steve Davis told BBC Radio Stoke:
"I'm delighted for everyone, the supporters and the staff, who have all worked very hard to get to this.
"It's a great achievement. And I'm proud of everybody. It's given everyone a lift.
"It was an exciting game and I'm delighted we came out on top. I hope everyone can make it to Wembley."
- 35 Belford
- 02 Clohessy
- 03 Gilbert (Hills - 32' )
- 06 Bilel
- 16 Prosser
- 23 Barker
- 04 Hall
- 07 Grant Booked
- 08 Timlin
- 24 Benyon (Harris - 54' )
- 37 Eastwood
- 01 Morris
- 12 Ferdinand
- 34 Hills
- 14 Martin
- 09 Harris
- 01 Phillips
- 02 Tootle
- 03 Davis Booked
- 05 Artell
- 06 Dugdale
- 04 Westwood
- 07 Bell
- 17 Mellor
- 10 Leitch-Smith Booked (Clayton - 75' )
- 11 Moore
- 25 Powell Booked
- 13 Martin
- 12 Shelley
- 15 Martin
- 34 Bodin
- 19 Clayton
Live Text Commentary
Full Time The game is over, as the referee blows his whistle.90:00 +1:07
The ball is sent over by Lee Hills, Header from deep inside the penalty area by Bilel Mohsni goes harmlessly over the crossbar.90:00 +0:57
Centre by Sean Clohessy, clearance made by Byron Moore.90:00 +0:25
Ryan Hall crosses the ball, clearance by Harry Davis.88:58
Sean Clohessy concedes a free kick for a foul on Kelvin Mellor. Direct free kick taken by Matt Tootle.88:02
Lee Hills delivers the ball, Adam Dugdale manages to make a clearance.87:01
Ryan Hall provided the assist for the goal.87:01 Goal scored
Goal! - Chris Barker - Southend 2 - 2 Crewe Chris Barker finds the back of the net with a headed goal from close in. Southend 2 (2)-(3) 2 Crewe.86:58
The ball is crossed by Ryan Hall,86:51
Centre by Ryan Hall, David Artell makes a clearance.85:31
Assist on the goal came from Nick Powell.85:31 Goal scored
Goal! - Max Clayton - Southend 1 - 2 Crewe Goal scored by Max Clayton from inside the penalty box to the bottom right corner of the goal. Southend 1 (1)-(3) 2 Crewe.84:19
The assistant referee flags for offside against Bilel Mohsni. Steve Phillips takes the free kick.84:01
Outswinging corner taken by Ryan Hall from the left by-line, Matt Tootle makes a clearance.83:15
Lee Hills sends in a cross, Bilel Mohsni takes a shot. Save made by Steve Phillips.81:03
The ball is delivered by Sean Clohessy, Headed effort from deep inside the penalty area by Freddy Eastwood misses to the left of the goal.79:51
Outswinging corner taken left-footed by Ryan Hall from the left by-line, Bilel Mohsni produces a header from inside the area that goes over the crossbar.79:20
Handball by Kelvin Mellor. Ryan Hall takes the direct free kick.79:04
Matt Tootle has an effort at goal from just inside the box that misses to the left of the goal.77:04
Free kick awarded for a foul by Nick Powell on Anthony Grant. Cameron Belford restarts play with the free kick.
Substitution Max Clayton joins the action as a substitute, replacing Ajay Leitch-Smith.73:18
Direct free kick taken by Adam Dugdale.73:18 Booking
Booking Anthony Grant shown a yellow card.73:15
Foul by Anthony Grant on Lee Bell, free kick awarded.72:21
Nick Powell has an effort at goal from close in which goes wide of the left-hand upright.70:55
The ball is crossed by Michael Timlin, save by Steve Phillips.70:22
Cameron Belford takes the free kick.70:22 Booking
Booking Nick Powell goes into the book for unsporting behaviour.67:41
Lee Hills crosses the ball, Ryan Hall takes a shot. Comfortable save by Steve Phillips.67:02
Nick Powell is ruled offside. Cameron Belford restarts play with the free kick.65:31
The referee blows for offside against Bilel Mohsni. Steve Phillips restarts play with the free kick.65:03
Bilel Mohsni takes a shot. Blocked by Adam Dugdale.64:20
Effort from the edge of the area by Nick Powell goes wide of the right-hand upright.63:25
Assist on the goal came from Chris Barker.63:25 Goal scored
Goal! - Neil Harris - Southend 1 - 1 Crewe Neil Harris scores a goal from close range low into the middle of the goal. Southend 1 (1)-(2) 1 Crewe.63:18
Chris Barker crosses the ball, save by Steve Phillips.62:24
Lee Hills takes the direct free kick.62:24 Booking
Booking Harry Davis goes into the book for unsporting behaviour.62:22
Free kick awarded for a foul by Harry Davis on Michael Timlin.61:14
Nick Powell produces a right-footed shot from just outside the box that misses to the right of the goal.60:00
Effort on goal by Ryan Hall from just outside the area goes harmlessly over the target.59:12
Nick Powell crosses the ball.58:18
The ball is sent over by Bilel Mohsni, clearance made by Kelvin Mellor.57:54
The ball is delivered by Byron Moore.57:07
Unfair challenge on Nick Powell by Anthony Grant results in a free kick. Adam Dugdale restarts play with the free kick.56:05
Effort from outside the penalty box by Freddy Eastwood hits the post.55:03
Freddy Eastwood takes a shot. Save by Steve Phillips.54:51
The ball is sent over by Ryan Hall, clearance made by David Artell.53:13 Substitution
Substitution Neil Harris comes on in place of Elliot Benyon.52:56
Michael Timlin has an effort at goal from just outside the box that bounces off the post.51:59
Effort from the edge of the penalty box by Nick Powell goes wide of the right-hand upright.49:46
Corner taken right-footed by Ashley Westwood from the right by-line to the near post, clearance by Lee Hills.48:56
Lee Hills is adjudged to have handled the ball. The free kick is delivered right-footed by Ashley Westwood from right wing, clearance made by Anthony Grant.48:39
Nick Powell takes a shot. Blocked by Luke Prosser.47:10
Corner taken right-footed by Ashley Westwood from the left by-line, Bilel Mohsni manages to make a clearance.46:57
Byron Moore takes a shot. Save by Cameron Belford.45:01
The referee gets the second half started.45:00 +2:18 Half time
Half Time The first half comes to an end.42:14
Lee Hills sends in a cross.36:23
The ball is crossed by Sean Clohessy.35:14
Steve Phillips restarts play with the free kick.35:14 Booking
Booking Booking for Ajay Leitch-Smith for unsporting behaviour.34:35
Ryan Hall produces a cross, clearance made by Adam Dugdale.33:44
Effort on goal by Byron Moore from just inside the penalty area goes harmlessly over the target.31:38 Substitution
Substitution Lee Hills on for Peter Gilbert.30:33
Ryan Hall takes a shot. Save by Steve Phillips. The referee blows for offside. Steve Phillips takes the indirect free kick.26:29
Anthony Grant concedes a free kick for a foul on Nick Powell. Direct free kick taken by Steve Phillips.25:33
The official flags Ajay Leitch-Smith offside. Cameron Belford takes the indirect free kick.23:49
Assist by Ashley Westwood.23:49 Goal scored
Goal! - Ajay Leitch-Smith - Southend 0 - 1 Crewe Ajay Leitch-Smith grabs a goal from the edge of the penalty area to the bottom right corner of the goal. Southend 0 (0)-(2) 1 Crewe.22:44
Free kick awarded for an unfair challenge on Michael Timlin by Ashley Westwood. Michael Timlin takes the direct free kick.21:35
Unfair challenge on Kelvin Mellor by Elliot Benyon results in a free kick. Steve Phillips restarts play with the free kick.20:53
Freddy Eastwood takes a shot. Kelvin Mellor gets a block in.20:30
Byron Moore produces a cross.18:52
Corner taken left-footed by Ryan Hall, Kelvin Mellor manages to make a clearance. Effort on goal by Sean Clohessy from just outside the penalty area goes harmlessly over the target.18:03
Ryan Hall crosses the ball, David Artell makes a clearance.16:38
Ashley Westwood sends in a cross, clearance by Ryan Hall.15:28
Shot by Nick Powell. Comfortable save by Cameron Belford.14:42
The ball is crossed by Sean Clohessy, Steve Phillips makes a save.12:28
Bilel Mohsni challenges Harry Davis unfairly and gives away a free kick. Steve Phillips takes the free kick.12:14
Bilel Mohsni produces a cross, Elliot Benyon takes a shot. Blocked by Adam Dugdale.10:52
The assistant referee flags for offside against Elliot Benyon. Steve Phillips restarts play with the free kick.10:44
The ball is delivered by Bilel Mohsni, clearance by Matt Tootle.6:59
Effort on goal by Lee Bell from long range goes harmlessly over the bar.6:24
Ashley Westwood takes the outswinging corner, Bilel Mohsni manages to make a clearance.5:45
Free kick awarded for an unfair challenge on Lee Bell by Anthony Grant. Ashley Westwood takes the direct free kick.5:12
Bilel Mohsni takes a shot. Steve Phillips makes a comfortable save.3:59
Foul by Michael Timlin on Matt Tootle, free kick awarded. Ashley Westwood restarts play with the free kick.2:38
The ball is delivered by Ryan Hall.1:20
Centre by Freddy Eastwood, Byron Moore manages to make a clearance.0:00
The referee starts the match.
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