Joe Leesley's 90th minute winner ensured Town progressed to the Buildbase FA Trophy First Round after a whirlwind second half at Blackwell Meadows.After an uneventful first 45, the contest sparked into life as both Reece Styche and Leesley converted spot kicks within the first ten minutes of the restart.
On loan Bradford City defender Lachlan Barr headed his side into the lead not long after, but Styche's 82nd minute finish looked to have set up a Tuesday night replay.
That was until the 90th minute when Leesley darted to the near post to meet George Thomson's corner and send Town fans home happy.
Simon Weaver handed a debut to on loan Guiseley striker Frank Mulhern, while Louie Swain was involved in the first team squad for the first time since March after eight months out injured.
Darlington made a bright start to the contest on what was a blisteringly cold night at Blackwell Meadows, though neither side could create any meaningful early chances.
It took until the 23rd minute for the contest's first shot to arrive, but Luke Trotman's effort never looked like hitting the target.
Liam Agnew tried his luck from 30 yards five minutes before half time, but couldn't hit the target as the referee brought an uneventful first half to a close.
Five minutes after the restart Greg Mills raced into the Town area before being brought to the ground, allowing Styche to coolly convert the subsequent penalty and give his side the lead.
Town were awarded a penalty of their own just five minutes later as Josh Falkingham cleverly flicked the ball into the path of Thewlis, who was brought down by Wilczynski; allowing Leesley to level the score.
Four minutes later Barr marked his Town debut with a goal and turned the contest on its head as the towering central defender headed home Leesley's right wing cross.
If the first half was dull, the second half was turning out to be anything but and could have been 2-2 after 61 minutes if Styche had not missed a guilt edged chance at the far post.
The hosts needed a goal to keep their hopes of going far in the Trophy alive, but Town were next to try their luck as both Mulhern and George Thomson went close.
The hosts remained in the contest and got their rewards for staying resilient as Styche bundled his way in behind the Town defence and finished low past Belshaw to level after 82 minutes.
The tie looked to be heading to a Tuesday night replay until the 90th minute when Leesley darted to the near post to meet George Thomson's corner and send Town through to the First Round.
Harrogate Town: Belshaw, Vann, Swain, Falkingham, Kennedy (Barr 38), Burrell, Thomson, Agnew, Mulhern (Hudson 79), Thewlis, Leesley
Subs not used: Cracknell, Gooda, O'Hanlon
Goals: Leesley 55(p), 90, Barr 59
Darlington: Wilczynski, Trotman, Galbraith, Turnbull, Collins, Brown, Mills (Gillies 81), Portas (Saunders 79), Styche, Syers, Thompson (Caton 81)
Subs not used: Vaulks, Bancroft
Goals: Styche 50(p), 82
Referee: B Speedie