Giuliano Grazioli and Ben Strevens both netted second half goals to allow Barnet to steal all three points at The Shay.
Halifax led at half time but the Bees pulled off a classic sting to stay on course for the play-offs.
Halifax dominated a first half played at break neck speed.
They could have led as early as the tenth minute when a quick free-kick from assistant manager and full back Sean McAuley allowed the impressive Ryan Mallon to fire in a cross, but Christian Lee's shot was off target.
The Shaymen were playing exhibition football at times spraying balls the length and breadth of the park and stringing together intricate but deadly passing moves.
But it was from a goalmouth scramble the breakthrough finally came.
A McAuley free-kick 20 yards from goal was saved by Bees keeper Shane Gore but he could only parry to the edge of the six-yard box, where Lewis Killeen was first to react blasting home.
But it was not all flare and finesse. For the second game in a row Halifax were involved in a mass brawl. On Boxing Day against Scarborough they had two players ordered off, but this time only Lee picked up a caution.
It was all change after the break as Barnet returned to the field a different team.
And quickly they levelled. Strevens burst clear on the right and slid a clever ball into Grazioli, who deftly chipped the ball over keeper Mark Cartwright for his 12th goal of the season.
Ten minutes later the Bees were in front. Captain Ian Hendon blasted a fierce 30-yard thunderbolt straight at Cartwright ,but he couldn't hold it.
Barnet then sat back and protected their lead frustrating Halifax right up until the final whistle.
Deep into injury time Val Owen's 20-yard volley could have tested a nervous looking Gore, but it was tantalisingly off target.
Halifax manager Chris Wilder said he thought his side threw the game away after an excellent first-half performance.
"The difference between the sides is that we had eight or nine good chances and scored once and they had two and scored them both," he said.