Mark Beck struck in the 89th minute to seal Yorkshire derby bragging rights and ensure Town left second place Halifax with all three points.
Simon Weaver made three changes from Saturday’s draw at Maidenhead as George Thomson, Mark Beck and Jack Muldoon replaced Jack Diamond, Sam Jones and Jon Stead.
Thomson, making his first start of the season, was involved from the outset, winning a free kick in a good position and almost finding the head of Beck, with Ryan Fallowfield also trying his luck early doors.
Halifax attacker Liam Mcalinden demnstrated why he is his side's top scorer inside the opening 15 minutes with a long range effort that wasn't far off nestling in the top corner.
Alex Bradley then forced the first save of the evening as Sam Johnson pushed away the midfielder's curling effort, with Halifax able to scramble away the resulting corner that Beck had guided goalwards.
Next it was the turn of James Belshaw to make an impressive save as Town's stopper twice denied Mcalinden with his feet, the second from a low free kick that had crept under the wall.
With nine minutes of the half remaining, Brendan Kiernan rolled the ball back to Warren Burrell just outside the area from where Town's Captain was desperately unlucky not to open the scoring as his effort rebounded back off the bar.
Town did have the ball in the net two minutes later through the unlikely source of Ryan Fallowfield, who had converted George Smith's low cross at the far post, only to see his celebrations cut short by the linesman flagging for offside.
Harrogate were the ones knocking on the door in the closing stages of the half, though Johnson's save from Beck's glancing header four minutes from time ensured the tie remained goalless.
The start of the second half was more even than the end of the first, with Will Smith making a crucial sliding block to deny the lively Mcalinden.
The hosts' main threat was coming from long range efforts, with Michael Duckworth almost catching Belshaw out not long before substitute Cameron King fired just over the bar.
The winning goal almost arrived from a Halifax set piece as Belshaw couldn't keep hold of a corner under intense pressure, but Town got bodies in the way and prevented the ball crossing the line.
With just one minute left to play, Fallowfield and Thomson combined down the right, with Thomson's low cross eventually falling to Beck from where he was able to poke over the goalkeeper and seal all three points!
Harrogate Town: Belshaw, Fallowfield, G Smith, Burrell, Thomson, Beck, Kiernan (Diamond 69), Bradley (Brown 80), Muldoon, Hall, W Smith
Subs not used: Emmett, Cracknell, Stead
Goals: Beck 88
Halifax: Johnson, Duckworth, Binnom-Williams, Clarke, Nolan, Sho-Silva, Staunton, Mcalinden, J King (C King 67), Williams (Southwell 72), Cooper
Subs not used: Earing, Appleyard, Hanson
Referee: S Mather