The Bees went into the half time break a goal ahead after John Akinde had headed the Bees into a 25th minute lead, but Orient were denied from the penalty spot two minutes after the restart when Lloyd James' spot kick was parried away by Jamie Stephens.
Moments later Sam Togwell made it 2-0 to the hosts with a deflected shot from outside the box, before Akinde claimed his second of the afternoon on the 58th minute.
For the short trip to Barnet player-manager Kevin Nolan made two changes to the side that drew 1-1 at York the weekend before as Lloyd James and Calaum Jahraldo-Martin came into the side for Sean Clohessy, who dropped to the bench, while Jobi McAnuff was ruled out with a calf injury.
Following four matches out through suspension Club captain Mathieu Baudry returned to the bench, and with vice-captain Clohessy also amongst the substitutes the armband was handed to James on his first start since December.
A close start to the match saw both sides look to slowly settle into the tie, though it was the hosts who had the first chance of the afternoon when Curtis Weston headed Elliott Johnson’s cross over after nine minutes.
Weston then flashed a left-footed strike wide of the far post moments later, but it was midway through the half when the hosts took the lead after striker John Akinde headed James Pearson’s ball in back across and into the bottom far corner.
Prior to the goal Orient had yet to test Jamie Stephens in the Bees goal, but moments after the goal midfielder Nigel Atangana was denied his first goal for the Club when the Barnet stopper produced a brilliant stop to keep out his powerful drive.
Soon after Stephens was then breathing a huge sigh of relief as his poor punch from Jerome Binnom-Williams’ free-kick into the box dropped to Shaun Brisley who made a hash of his effort and sliced it well wide.
Stephens certainly made up for the error quickly however with 38 minutes on the clock he produced yet another great stop to frustrate Atangana who had powerfully driven a shot towards goal after Binnom-Williams’ cross was only headed as far as the Frenchman on the edge of the box.
Having gone into the break a goal down, Orient returned for the second half unchanged and within two minutes of the restart were awarded a penalty when Binnom-Williams went down under the challenge of Andy Yiadom.
Captain for the day Lloyd James took up the responsibility of taking the spot kick, but was unable to convert as Stephens guessed correctly to dive to his left and parry the shot away before Calaum Jahraldo-Martin headed the rebound over.
Two minutes later the miss was to prove costly as Barnet doubled their lead. Akinde first muscled his way beyond Peter Ramage and saw a shot parried away by Alex Cisak. Luke Gambin rattled the crossbar with his follow up before Weston flicked the ball on for Sam Togwell 20 yards out who then saw his shot deflected beyond Cisak and into the bottom corner.
With just under an hour played it was then 3-0 to Barnet as Akinde claimed his second of the afternoon after chasing a long ball forward and getting there before Cisak to flick a header into an empty net.
First-year scholar Josh Koroma was then handed his debut on the 63rd minute when the young winger came on for player-manager Kevin Nolan to take up a position on the left, with Jahraldo-Martin moving across to the right.
Needing a quick response Ollie Palmer then directed a header wide from a James cross, and with just over 20 minutes remaining Orient made their second substitution as Armand Gnanduillet replaced Jay Simpson.
With 10 minutes remaining the substitute went on a powerful run to burst into the Barnet box, but was unable to pull a goal back as he could only poke an effort wide.
Koroma was looking impressive for the O's out on the left and with four minutes remaining the 17-year-old cut inside and curled a shot into the hands of Stephens before Gnanduillet drilled a low shot inches wide of the post.
Four minutes stoppage time was then indicated by the fourth official, and despite Koroma curling an effort just over the bar Orient were unable to grab a consolation as they slipped down to 11th in League Two and two points off the Play-Off places with five games left to play.
BARNET: Stephens, Pearson, Dembele, Nelson, Johnson, Yiadom, Togwell, Weston (Stevens 81), Gambin (Muggleton 85), Gash (Shomotun 63), Akinde
SUBS: Stack, N’Gala, Sesay, Champion
GOALS: Akinde (25 & 58), Togwell (49)
BOOKED: Weston (15), Togwell (56)
ORIENT: Cisak, Hunt, Brisley, Ramage, Binnom-Williams, James (C), Atangana, Nolan (Koroma 63), Jahraldo-Martin, Palmer, Simpson (Gnanduillet 68)
SUBS: Gregory, Baudry, Shaw, Clohessy, Turgott
BOOKED: Palmer (73)
REFEREE: Keith Stroud
ATTENDANCE: 3,401 (1,655 Orient supporters)