Ruel Sotiriou struck in the first half and James Alabi in the second before Charley Barker pulled on back for the home side.
Orient got the cup tie underway but Haringey Borough registered the first clear chance on goal when Charley Barker pounced upon the loose ball in the box but fired in to the side netting from close range.
The hosts were on the attack not long after, Joel Nouble broke into the box from the left but lost his footing as he went to shoot and sliced the ball wide of the target.
The first clear chance for the O’s came after 20 minutes, Ruel Sotiriou smartly found Hector Kyprianou on the edge of the box but the midfielder curled his effort over.
Orient took the lead through Ruel Sotiriou shortly after the half hour mark, the forward pounced upon the ball as it rolled clear of the box and placed it into the bottom corner of the net.
Immediately after the restart, Brendon Shabani’s lobbed attempt from 20-yards almost caught out Austin Byfield but the Haringey ‘keeper scrambled back to tip the ball over the bar.
As the opening half drew to a close, Karl Akinwande linked up with Barker inside the box before he watched the ball creep wide of the far post.
After a quiet start to the second half, Kyprianou looked to spark some life in to the game when his well-timed attempt from distance forced an excellent save from Byfield in the Haringey Borough net.
Akinwande’s shot from the edge of the box flashed over the bar and out for a corner with the help of a George Elokobi deflection.
Haringey came inches away from a leveller after 75 minutes. Nouble’s driven shot from wide pinged off the inside of the post and rolled across the line before ‘keeper Arthur Janata smothered the danger.
Orient doubled the four minutes from time after they had soaked up the pressure from Haringey. Ruel Sotiriou’s stinging effort from range forced the ‘keeper to parry in to the path of Alabi who swept the ball home from six-yards.
The hosts pulled a goal back two minutes later through former O Charley Barker who drilled home after the O’s failed to clear their lines.
On the stroke of full-time, Alabi’s excellent flick on found the run of Sotiriou who was through on goal, but the forward was brought down before he could test the ‘keeper. Full-back Scott Mitchell was dismissed for the challenge as he was the last man.
Haringey battled well in the closing stages but Orient defended their lead well and progressed to the Quarter Final stages of the London Senior Cup.
ORIENT: Janata, Fleming, Sweeney, Lawless, Elokobi, Happe, Kyprianou, Shabani, Harrold, Alabi, Sotiriou
SUBS: Byrne, Sivi, Phillips, Clayden, Haxhiu
BOOKED: Lawless (39)
GOALS: Sotiriou (32), Alabi (86)
HARINGEY: Byfield, Olufemi, O’Donaghue, Richards, Mitchell, Stone (Sappleton 69), Akinwande, Staunton, McKenzie (McDonald 66), Barker, Nouble
SUBS: Edwards, Kirby, Pajetat
GOALS: (Barker 88)
RED: Mitchell (90)