In injury time Alasan Ann squeezed a shot under Ferdinand but Bentley was able to stoop down to collect and, with the scores remaining level, the hosts began the second period hunting a goal. Within seconds of the restart, Abdellah had beaten Blake for pace, only to see a fierce shot blocked, and on 52 minutes Anthony Furlonge's downward header was ushered away from goal by Dasilva.
At the mid-point of the second period, Town's first meaningful attempt of the half flew over the crossbar courtesy of Patrick's speculative 25-yarder, but there was to be greater concern for Blues when substitute Lyle Della-Verde sold Bentley short with a simple pass and the 'keeper had to react quickly to beat Ann to the loose ball. In the process of doing so, he jarred his right leg and received considerable treatment before, with understudy Luke Chambers already sidelined through injury, he decided to continue.
He managed to save from Christian Tavernier's long-range effort, with Kidd also staying alert in the Hatters goal to push Teddy Nesbitt's cross-shot over, before a frantic end to the regulation 90 minutes saw Louis Baucutt recover his composure after slipping to hustle Ann off of the ball and allow Bentley to gather. Play quickly switched to the other end and Abdellah rifled a shot into the gloves of Kidd.
With just two minutes remaining, Furlonge spotted the 'keeper off of his goalline and attempted an audacious 35-yard lob, but Kidd back-peddled to claim above his head. There was an anxious moment at the back for Southend when Lacey nodded Matt James' deep free-kick across goal, but Ann could not stretch far enough to convert, and Patrick's endeavours to turn the ball home were thwarted by Bentley's outstretched leg.
Even then, in the third minute of stoppage time, the action did not let up, and Ofori-Acheampong could have settled the tie without recourse to a further thirty minutes had he not miskicked in front of goal following Della-Verde's fleet-footed work.
Extra time was required, though, and 15-year-old Della-Verde saw an effort slide across the face of goal from the left-hand side of the penalty area after good link-up play from Ofori-Acheampong and Smith. The winger then turned provider, crossing dangerously before the ball was pushed out to Stevens on the edge of the penalty area. The cultured midfielder was unable to find the target as he flashed over in the 102nd minute of play.
Sixty seconds later, Southend edged in front for the first time. Both Stevens and Woodyard scrapped for the ball in midfield before Ofori-Acheampong used his considerable strength to bounce off of a challenge and blast towards goal, his shot taking a wicked deflection to spiral over Kidd and into the net for his eighth goal of the season.
In first-half injury time Smith put further ground between the two Football League Youth Alliance sides as Della-Verde found Ofori-Acheampong on the left-hand side. Instead of trying his luck himself and potentially notching a hat-trick, he played a simple pass to the Republic of Ireland Under-18 international who slotted past Kidd.
The imperious Ferdinand blocked Cauley Woodrow's 30-yard piledriver before Kidd made a smart save from Ofori-Acheampong. The towering striker then almost provided an assist for Woodyard, but the second-year scholar's slammed finish was ruled out by the raising of the assistant referee's flag.
Disappointingly the match ended on a sour note as Della-Verde, who had tormented his opponents with a combination of silky skills and dextrous turns since being introduced in the 68th minute, was unceremoniously scythed down from behind by Ann, who was immediately dismissed.
Nonetheless, Southend enjoyed a safe passage into the Second Round for the first time since 2007/8, where they will face Brentford at Roots Hall, the Bees having defeated Concord Rangers 5-0 at Thames Road. The match is due to be played by Saturday 20th November.
Southend United U18s: Daniel Bentley, Anthony Furlonge, Teddy Nesbitt, James Stevens, Louis Baucutt, Kane Ferdinand, Hicham Abdellah (Ryan Auger 106), Alex Woodyard, Duane Ofori-Acheampong, George Smith (Michael Hyland 108), Julian Okai (Lyle Della-Verde 68).
Substitutes not used: Rhys Mackay, Jack Paxman.
Goals: Ofori-Acheampong (39, 103), Smith (105+1).
Cautioned: Della-Verde (90+4 - foul tackle), Smith (105+1 - goal celebration), Ofori-Acheampong (120+3 - adopting an aggressive attitude).
Luton Town U18s: Lewis Kidd, Matt James, Mason Blake, Christian Tavernier (Fabio Bufano 97), Alex Lacey, Newman Carney, Jordan Patrick, Michael Cain (Liam Toomey 68), Alasan Ann, Cauley Woodrow, Ryan Dasilva (Colby McAdams 106).
Substitutes not used: Mustafa Mirzai, Moses Nakabaale.
Goal: Patrick (33).
Dismissed: Ann (120+2 - serious foul play).
Cautioned: Patrick (87 - foul tackle), Bufano (120+3 - adopting an aggressive attitude).