Two goals in the space of three second half minutes from Ricardo Santos helped Barnet see off the O's 3-1.
After a goalless first half Santos slotted home two close range finishes to put them in command and although Paul McCallum gave Orient hope, Curtis Weston struck in stoppage time to seal the win.
The O’s made two changes to the side which lost 4-0 at Exeter City on Monday, with Josh Koroma coming in for his first league start alongside a return for Teddy Mezague in place of the injured Sandro Semedo and Ollie Palmer, who dropped to the bench.
Orient forced the first corner of the game, but it was the visitors who had the first chance of the game when Curtis Weston’s ball in from the right should have been connected with by either Mauro Vilhete or top goalscorer John Akinde, however, both missed the cross.
Koroma was positive from the off in his first league start and with eight minutes on the clock he drifted inside and got a shot away. Jamie Stephens could only push the shot into the path of Nigel Atangana but the midfielder couldn’t quite connect with the loose ball.
That was Stephens’ last action of the game as he was forced off through injury and was replaced by Josh Vickers.
Michael Collins, playing just behind Paul McCallum, continued to pull the strings and with 20 minutes on the clock he was urged to shoot by the home faithful. Shoot he did, but the effort was tipped wide by Vickers.
Akinde is always a menace for opposing defences and he got his head on a right-wing cross. The striker tried his best to force it back across goal and he did just that, but none of his team-mates were able to connect.
Barnet had been kept quiet for the most part but Alex Cisak in the O’s goal was forced into his first save of the afternoon when tipping Simeon Akinola’s curling left-footed effort behind for a corner.
The double ‘Akin’ up top were causing problems though and with 34 minutes on the clock Akinde’s brute strength saw him shrug off the attentions of Parkes before getting a shot away. Cisak was equal to the effort and when the rebound fell to the striker he failed to control the ball and it was behind for a goal kick.
Akinde should have opened the scoring for the Bees just short of half-time. Collins was dispossessed and the striker tussled with Yvan Erichot.
Erichot and Akinde come together with the striker just keeping his balance. He was now clean through on goal, but his shot from just inside the box was wide of the target, much to the relief of the O’s.
Cisak was forced into action again late in the half as he did superbly well to tip away Vilhete’s effort after the winger had ghosted in off the left. It was all the more of a save with the keeper already diving the other way.
No changes were made at the break by either side, and chances in the early stages of the half were few and far between.
Orient enjoyed most of the possession without testing Vickers, and the closest either side came was when Massey drifted in of the left and fired an effort just over the bar with Vickers at full stretch.
That proved to be the catalyst for opportunities though as Barnet opened the O’s up and Akinde’s cross found the diminutive Vilhete and his header was off target.
But the visitors were to break the deadlock though just after the hour mark when a header at the back post was spilt by Cisak and Santos was on hand to tap home from close range.
No sooner was it 1-0, it became 2-0 and it was that man Santos again three minutes later. Nana Kyei played the ball across and Santos was there to stroke it home once more.
Fresh from the second goal, Ollie Palmer was introduced in place of the booked Mezague, before Ulrich Nnomo replaced Koroma.
Palmer had his first chance to pull a goal back with 12 minutes to go when he turned on the ball but saw his shot deflected behind for a corner.
And from that set piece the O’s pulled one back when Kennedy’s inch perfect corner was met by the head of McCallum who headed past Vickers to give Orient hope.
Time was running out though and a minute from time a Collins cross was flicked on by the boot of McCallum but the onrushing Atangana couldn’t beat Vickers to the ball.
But that hope was extinguished in stoppage time when the Bees made a breakaway. Campbell-Ryce’s shot struck the bar and Curtis Weston was there to slot home the rebound to seal the three points.
ORIENT: Cisak, Hunt (c), Parkes, Erichot, Kennedy, Mezague (Palmer 67), Massey, Atangana, Collins, Koroma (Nnomo 73), McCallum
SUBS: Sargeant (GK), Bowery, Moncur, Pollock, Judd
GOALS: McCallum (79)
BOOKED: Mezague (25), Hunt (90+4)
BARNET: Stephens (Vickers 9), H Taylor, Nelson (c), Santos, Johnson, Weston, Vilhete, J Taylor, Kyei (Champion 70), Akinola (Campbell-Ryce 61), Akinde
SUBS: Gambin, Muggleton, Nicholls, Tutonda
GOALS: Santos (63, 66), Weston (90+2)
REFEREE: Andy Haines
ATTENDANCE: 4,642 (730 Barnet fans)