Ten man Orient enjoyed penalty shootout drama to advance to the second round of the Carling Cup.
Michael Richardson gave Orient the lead 22 minutes in, rising high to head home an Alex Revell cross.
The hosts levelled shortly after, with Mark Phillips heading in a Ryan Hall free kick to see the sides all square at the break.
Jonathan Téhoué was shown a straight red card on the hour mark, and with Southend unable to make the most of their numerical advantage, the game went to extra time and eventually a penalty shootout.
Russell Slade made two changes for the clash at Roots Hall, with Richardson getting his first start in an O’s shirt, while Jonathan Téhoué also came in.
Newcastle loanee Richardson started in place of the injured Leon McSweeney, while Téhoué replaced Jamie Cureton who dropped to the bench.
Téhoué was paired up front with Revell who was returning to one of his former clubs.
Slade named six subs, including young keeper Tom Lovelock and Terrell Forbes, making his first appearance in the matchday squad having missed the entire pre-season campaign following an operation on his digestive system.
Southend started with former Orient keeper Glenn Morris between the sticks, while Saturday’s goalscorer Bilel Mohsni was amongst the substitutes.
Both sides made a lively start but it was the hosts who caught the first sight of goal seven minutes in.
Finding space, winger Hall didn’t need to be asked twice to run at goal before firing off Ben Chorley but Lee Butcher was a match to the effort.
Orient hit back though when Téhoué linked well with Revell but the former Southend man saw his shot drift wide of the right hand post.
The visitors suffered a scare on 18 minutes when Elliot Omozusi’s back pass fell short of Butcher but former Millwall forward Neil Harris was unable to convert, lifting his effort over the bar.
The O’s reply was immediate again, as Richardson showed good strength to create an opening for Téhoué, who’s low drive was parried by Morris.
Their pressure turned to a lead shortly after when Richardson headed in on 22 minutes.
The Newcastle youngster rose highest unmarked in the box to head home Revell’s cross, powering beyond Morris.
The one goal lead could have been extended just a minute later with Richardson again at the heart of the action.
After Téhoué saw his effort rebound to the 19-year-old, the follow up shot was again blocked as the O’s looked to turn the screw early on.
The visitors were pegged back on the half hour though when Phillips found himself unmarked to head in.
The defender ghosted into the box to meet Hall’s free kick and sent a strong header beyond Butcher.
Hall was proving the threat for the hosts and the winger went close twice just before the break, firing wide of both posts when given the space to turn.
The hosts saw the first chances of the second half when Harris’ header drifted wide before Hall again ran at the defence but provided Butcher with an easy save to make.
Orient were reduced to ten men on the hour mark when Téhoué was given his marching orders for a head butt on Shrimpers defender Luke Prosser, leaving Slade’s side with an uphill struggle.
The hosts looked to make the extra man advantage count, pushing forward with Orient struggling to create any opportunities.
Southend were presented with a glorious chance to win the match on 81 minutes when a mix up between centre back pairing Chorley and Scott Cuthbert saw a loose ball fall to substitute Lee Sawyer but the former Chelsea midfielder saw his stinging drive fall just wide.
With the clock ticking past 90 minutes, Hall sent in another powerful drive but Butcher was again a match to the effort as the match headed for extra time.
The first period of extra time burst into life nine minutes in when Butcher was forced into a fine double save, first denying Liam Dickinson before keeping Kane Ferdinand’s effort out.
Dickinson went close shortly after, looping a header over a flat-footed Butcher but was denied on the line by stand-in skipper Chorley.
Orient made a brighter start to the second period, having one last throw of the dice before a penalty shoot out and felt they should have had a penalty themselves.
George Porter was pulled down in the box but the referee was not convinced.
Butcher was called into action shortly after when Sawyer let fly with a volley but his low save ensured the scores stayed level as the match headed for penalties.
Southend Penalties: Dickinson, Saved. Harris, Scored. Clohessy, Scored. Kalala, Saved. Hall, Scored.
Orient Penalties: Omozusi, Scored. Daniels, Scored. Chorley, Scored. Richardson, Saved. Cureton, Scored.
Southend: Morris; Clohessy, Coughlan, Phillips (Mohsni 45), Prosser; Hall, Ferdinand (Grant 105), Kalala, Johnson (Sawyer 70); Harris, Dickinson.
Subs: Gilbert, N’Diaye, Bentley, Crawford.
Orient: Butcher; Omozusi, Chorley, Cuthbert, Daniels; Smith, Spring (Porter 76), Richardson, Cox (Forbes 107); Téhoué, Revell (Cureton 84).
Subs: Cestor, Odubajo, Lovelock.
Attendance: 4,847 (1,225)
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