Adam Morgan opened the scoring in the opening minutes and Tom Denton headed home a second for the visitors midway through the first half before Matthew Kosylo sealed the win with a penalty 16 minutes from time.
Head Coach Steve Davis made five changes following the previous defeat at Boreham Wood.
Josh Coulson, George Elokobi and James Dayton all missed out through injury, and were replaced by Jamie Sendles-White, Michael Clark and Romuald Boco respectively while Henry Ochieng and David Mooney made way for Alex Lawless and Matt Harrold.
Alex Lawless captained the O’s, but the hosts failed to get off to a bright start and found themselves behind on the fiftth minute Adam Morgan smashed home from close range.
The first Orient chance came soon after, when Jobi McAnuff controlled and turned brilliantly inside the box before his clipped cross met the head of Matt Harrold, who’s header bounced the wrong side of the post.
The O’s began to grow in to the game well and should have equalised when Jake Caprice’s cross was parried in to the path of Romuald Boco who fired over from inside the box.
Again, the home side dominated possession and looked to level the scores when good play between Harrold and Macauley Bonne allowed the latter to get a left footed shot away that was eventually held by Samuel Johnson.
Since the visitors scored the opener, it had been all one-way traffic going in the Orient’s favour.
As a result of Caprice winning a corner, Bonne rose highest to meet the set-piece but the striker saw his effort land just wide of the far post.
Despite creating the most chances, FC Halifax Town doubled their lead when Tom Denton nodded in a curling free-kick just before the half hour mark.
The visitors had another big chance to make it three when the ball fell to Morgan inside the box, but the striker didn’t connect cleanly enough with his shot and the ball rolled wide of Charlie Grainger’s goal.
Ten minutes before half-time and the game was still very open, with chances being created thick and fast by both sides.
Bonne saw an effort held well by Johnson before Grainger produced a brilliant save to deny Denton his second of the night.
Minutes before the break, McAnuff’s long range bending shot had beat the ‘keeper but not the woodwork, the winger’s effort pinged back off the frame of the goal before being cleared by the visitors.
Both teams returned for the second half unchanged and the first chance fell to Halifax captain Matthew Brown who glanced a header wide moments after the restart.
A twisted run by McAnuff allowed him to make space before firing at goal, but the midfielder’s effort was deflected behind for a corner.
Another darting run upfield, this time by Caprice who raced past two men before his low cross was headed away but only in to the path of McAnuff who fired high over the bar.
With just less than half an hour remaining the boss made the first change when David Mooney replaced Boco and the forward stepped straight in to the action winning a free-kick in a dangerous position for the O’s.
Another great chance for the O’s came when Craig Clay was quickest to the ball and had beat the keeper before Bonne had an open shot on goal but the striker’s effort was blocked as FC Halifax defenders rushed back.
Orient continued to search for a goal and had two brilliant chances that fell to Mooney. The forwards attempted over-head kick was held by Johnson and the second attempt saw the ball chested down just outside of the box but poked wide.
But Against the run of play, it was FC Halifax who found the net as the visitors were awarded a penalty when the referee decided Joe Widdowson knocked over Morgan in the box.
Matthew Kosylo converted the resulting penalty and sent Grainger the wrong way.
With time running out Josh Koroma was introduced in place of Harrold for the final minutes, but the O’s were unable to even register a consolation in what proved to be a frustrating night in E10.
ORIENT: Grainger, Caprice, Sendles-White, Clark, Widdowson, Clay, Lawless (C), Boco (Mooney 61), McAnuff, Harrold (Koroma 86), Bonne
SUBS: Sargeant, Happe, Ochieng
BOOKED: Clark (71), Widdowson (87)
FC HALIFAX TOWN: Johnson, Wilde, Brown (C), Garner, Kosylo (Charles 89), Hotte, Denton, Oliver, McManus, MacDonald (Tomlinson 69), Morgan (Moyo 82)
SUBS: Nicholson, Lynch
GOAL: Morgan (5), Denton (29), Kosylo (74 pen)
BOOKED: Wilde (28), Kosylo (45), McManus (50)