Goals from Manny Duku and Devante Rodney put Halifax 2-0 up before Josh Koroma quickly got one back.
Conceding deep into added time was a cruel way for Town to be denied what would arguably have been their best result of the season, but Orient’s pressure finally told at the death.
Town may have been unchanged from their last game against Maidenhead, but were unrecognisable from that match, playing with far more intensity and enthusiasm, and can reflect on a very hard-earned point from a contest in which they certainly played their part.
Koroma’s low shot was saved by Sam Johnson’s foot within the first couple of minutes as the hosts made an ominously positive start.
Former Halifax loanee Craig Clay was then given too much space to fire just wide after a nice one-two with James Brophy.
Another shot by Koroma was comfortably saved by Johnson amid a purposeful start by Orient, who looked determined to make up for their midweek defeat at Bromley.
But it was Town who took the lead when Matty Kosylo found space on the left, and hit the post after cutting in on his right foot. The rebound fell to Duku, whose first effort was blocked before he bundled the ball in from close range.
That knocked Orient out of their stride, with the hosts a little more apprehensive and playing with less urgency after that.
The goal was undoubtedly a shot-in-the-arm for Town, who competed well and offered a threat when they broke forward, as shown when Cameron King picked out a lovely run by Duku, who fired over from just inside the box under pressure from Josh Coulson.
Johnson was called into action to tip the influential Clay’s driven shot onto his near post as the two sides went toe-to-toe in an entertaining contest.
Koroma brought another save from Johnson before the ball was scrambled away, as Orient racked up their efforts at goal with worrying regularity.
Charlie Lee was next to try his luck, but Johnson reacted well to tip his 20 yard shot away.
Tenacity from King won the ball inside the Orient half, before Kosylo strode forward and fired wide of the near post from just outside the box.
Orient’s top-scorer Macauley Bonne had been kept quiet by the ever-reliable Nathan Clarke and Matty Brown, with Duku and Devante Rodney causing far more problems, holding the ball up well and making good runs off the ball.
Rodney was given too much space to turn and size up a chance just before half-time, and made Orient pay in spectacular style with a rocket of a left-foot shot that flew across goal and into the far corner, as Orient conceded more than once at home for only the third time this season.
Town’s two goal lead was nice while it lasted, but it lasted less than a minute, as Koroma finally found the net with a well-struck rising effort from around the edge of the box after cutting in from the left.
That brought to an end a terrific half of football, in which Town had struggled to contain Orient at times, but through a combination of hard work, discipline and an incisiveness in attack, held an eyebrow-raising lead.
Johnson produced a superb save a few minutes after the restart to deny Brophy after Joe Skarz had blocked the winger’s initial effort.
Another couple of efforts by Koroma were saved by Johnson as Orient threatened an equaliser.
The hosts were building some real momentum as Jay Simpson diverted a cross into the path of Dan Happe, but the centre-back could only head over from four yards at the far post.
Town’s attacks were becoming less frequent as they began to be penned back; Kosylo got a sight of goal after a Town corner, but dragged his shot wide.
Orient’s momentum waned as the second-half went on though, and The Shaymen’s resilience seemed to grow the longer they remained in-front.
King and Rodney both got sight of goal from a corner with just over 10 minutes left, but both efforts were blocked.
After some brave blocks by Town defenders throwing themselves in-front of shots by the hosts, Kosylo had a chance to potentially put the win beyond doubt when Rodney played him in-behind Orient’s last man, but the Town winger scuffed his shot wide.
Orient went 4-2-4 to try and force an equaliser, and Harrold bundled the ball over the line from a corner as The Shaymen came within seconds of victory.
Leyton Orient: Brill, Lawless (Dayton 70), Coulson, Happe, Widdowson (Maguire-Drew 86), Brophy, Lee (Harrold 77), Clay, Koroma, Simpson, Bonne. Subs not used: Sargeant, Ling.
Scorers: Koroma (45), Harrold (90)
Shots on target: 13
Shots off target: 17
Halifax: Johnson, Hanson, Clarke, Brown, Skarz, Berrett, King, Staunton, Kosylo, Duku (Quigley 83), Rodney. Subs not used: Rowley, Preston, Edwards, Gondoh.
Scorers: Duku (9), Rodney (45)
Shots on target: 3
Shots off target: 10
Referee: Peter Gibbons
Town man of the match: Sam Johnson