Despite Ruel Sotiriou scoring within the first minute of play, the O’s were unable to hold their lead and conceded the equalising goal just before half time.
Danny Webb made one change to his starting XI from Tuesday’s Youth Alliance Cup win at Stevenage. Luca Carter-Henry slotted into midfield in the place of Sam Dalby who was rewarded for his goals with a place in the first team squad on Saturday.
Seconds after kick-off Sotiriou made a diagonal run to the right wing before squaring it to Charles Clayden who helped it further along to Luca Carter-Henry. The latter then drilled the ball back across the box for Sotiriou to tap in the opener.
Orient looked the stronger of the sides in the opening twenty minutes and went close through Sotiriou on two occasions. The first, a blocked shot which was diverted behind for a corner and the second was cleared off the line by a Southend defender after Sotiriou raced through on goal.
The O’s were made to pay as moments before half time, when Harry Cuthbert grabbed the leveller. Matt Rush cut the ball back to Cuthbert who managed to get a toe to the ball before Arthur Janata could make a save.
After the break, Andrew Camilo-Tayaca’s electric forward run allowed him to thread the ball to Hector Kyprianou, who got his shot on away form a tight angle but the ball flew just inches wide.
The visitors had a chance to take the lead when Emile Acquah directed a free header goal-wards but was denied by the superb strong palm of Janata who tipped the ball on to the crossbar.
With just over 20 minutes left on the clock, Charles Clayden darted up-field before he clearly slotted the ball over the line but the ball bounced back off the inner frame of the goal and was cleared by a Southend defender.
Orient players appealed to the referee that the ball had crossed the line before it hit the structure of the goal but the officials didn’t agree and waved play on.
That proved to be the difference in the game as Southend scored within minutes of the controversial decision.
Jon Benton was free in the middle and struck the ball from 25-yards out it bounced just before Janata could reach it and went into give Southend the lead.
The visitors stretched their lead further through Acquah. Benton won the ball in the box and played the ball to Acquah who floored Janata before he powered home a shot from close range.
Toby Stevenson looked to claw one back for the O’s late on when he glanced a header from an excellent Clayden free-kick, but the touch on the ball wasn’t enough to direct it towards goal.
The two second half goals from the visitors proved enough for them and they saw out the remaining minutes before the referee called for full time.
The O’s are next in action on Saturday when they welcome Northampton to Whitbreads.
ORIENT: Arthur Janata, Andrew Camilo-Tayaca, Teddy Perkins, Toby Stevenson, Alfie Fleming, Ernold Haxhiu, Hector Kyprianou, Luca Carter-Henry, Amin Benyoucef, Ruel Sotiriou, Charles Clayden
SUBS: Will Sanders, Samuel Amedu, Wynford Marfo