The game was goalless at half time, but three goals in the final half-hour of play saw the deadlock broke.
The opening ten minutes of the tie were quiet as both sides found their feet, however, Rhys Byrne had to be alert to beat an on rushing forward to the ball as the hosts threatened to counter early in the game.
The game sparked into life around the 15-minute mark and Byrne had to make an instinctive save to block a volley from inside the area.
Straight down the other end – Jayden Young displayed great fight to wriggle away from a defender before taking aim, but with the angle favouring the ‘keeper, the shot-stopper managed to beat the ball away from danger.
A long-range effort crashed against the underside of the Orient crossbar, before a heroic block denied Young from inside the area following great pressing from Brian Ifeanyi.
Both sides tried to steal a lead before the break, but both defences stood resolute before the ref signalled for half-time with the score at 0-0.
Jordan Adeyemi was introduced early in the second half and the forward injected a different dimension to Orient’s attack, but it would be United who found the opening goal.
On the hour mark a sharp break from the visitors down the right channel looked threatening, and the winger made the most of his opportunity, cutting inside and running into the area and placing an effort into the bottom corner.
Five minutes later the referee waved away a penalty claim from the O’s. Anthony Papadopoulos whipped a free-kick into a good area and Adeyemi looked to get on the end of it, but instead got tangled with his marker and hit the ground.
Adeyemi later tried to wrap a controlled effort past the ‘keeper from 25-yards but Southend’s number one turned the ball away for a corner.
With the match in the final quarter, Ben Staerck and Finlay Lovett were introduced from the bench as Kevin Frempong and Bradley McClenaghan made way.
The Seasiders doubled their advantage with ten minutes left to play. A ball bobbled across the box to a navy shirt who created half-a-yard for himself and unleashed a powerful strike into the top corner.
The second goal all but confirmed the win for the visitors but there was still time for Lovett to bag a consolation in injury time.
Adeyemi and Ifeanyi linked up well on the edge of the area, with the latter setting the ball up for sub Lovett. A first-time effort with the outside of his boot bent inside the post, with the ‘keeper rooted to the spot.
A fantastic finish from Lovett but too late in the game for the O’s to fight back and claim any points, as it finished 2-1 to Southend United.
Next up: Northampton Town (A)
ORIENT: R. Byrne, J. Sivi, W. Marfo, T. Francois-Vernal, D. Dubar-Bonnie, Kevin Frempong (Ben Staerck 71”), Bradley McClenaghan (Finlay Lovett 73”) Anthony Papadopoulos, Jayden Young (Jordan Adeyemi 59”), Brian Ifeanyi, Lawrence Hammond
GOALS: Lovett 90”