Ruel Sotiriou cancelled out a first half opener with a determined finish on the hour, though a penalty kick 25 minutes from time secured the victory for Southend.
Assistant Coach Ross Embleton and Youth Team Coach Danny Webb took charge of the side which consisted of a number of scholars as well as young professionals Sam Sargeant, Myles Judd, Michael Clark, Henry Ochieng, Freddy Moncur and Sam Dalby.
It was the hosts who stamped their authority early on, and the Shrimpers took the lead on the 7th minute when a shot from Harrison Reeves squirmed beyond the reach of Sam Sargeant in the O’s goal.
Strikers Ruel Sotiriou and Sam Dalby endured a frustrating opening period, though the former produced a neat turn to beat a Southend defender before dragging a shot wide of the far post on the 31st minute.
Moments later Dalby benefitted from an underhit backpass, but despite breaking into the box the ball got caught under his foot as the effort flew over the bar.
Following the interval Orient looked much more fluid in midfield and got their reward on the hour mark when Amin Benyoucef won the ball back inside the Shrimpers half and played it out wide to Freddy Moncur who delivered a cross which Sotiriou brought down well before showing great strength to shrug off a defender and find the bottom corner.
The match was not to be level for long however, as Southend were rewarded a penalty three minutes later when Michael Clark was adjudged to have tripped a winger on the byline. Renei Batlokwa stepped up to take the spot kick and sent Sargeant the wrong way to retore the hosts lead.
Not fazed by the goal, Orient continued to push forward and thought they had levelled the tie for a second time on the 74th minute when Moncur converted in the box after intercepting Henry Ochieng’s initial shot, though the goal was ruled out for offside.
Following the chance the O’s continued to push forward but were unable to find a way back into the tie despite several dangerous crosses flashing across the face of goal as Southend held on for the 2-1 victory.
ORIENT: Sargeant, Judd (Camilo-Tayaca 72), McLean, Clark, Stevenson, Ochieng, Moncur, Barker, Benyoucef (Clayden 84), Sotiriou, Dalby