Three goals in eight second half minutes saw Hartlepool come back from 2-0 down to keep up their league best home record and send Town home with a third defeat of the season.
Town had gone into the break 2-0 up through George Thomson and a Neill Byrne own goal, though it could have been more had Jack Diamond and Thomson not had goals ruled out either side of the break.
Pools capitalised on this in emphatic fashion with David Ferguson, Mark Cullen and Matty Daly all finding the net to put the hosts ahead and in a position they would hold until full time.
Both sides made one change from their midweek fixtures with Lloyd Kerry replacing Alex Pattison for Town and Jonothan Mitchell taking the place of Ben Killip in the Pools goal.
With a big home crowd behind them, Hartlepool crafted the first chance of the afternoon when Mark Cullen found space in a good position, but could only drag wide of goal.
Mark Oxley was then called into action to prevent Hartlepool's strong start giving them the lead after he kept out Luke Hendrie's header with a diving save.
The home side were looking the more likely in the opening quarter of an hour and had the ball in the net through Neill Byrne, but the Hartlepool man was adjudged offside when he tapped the ball home from a yard out following a well worked short corner.
Harrogate managed to get a foothold in the game after the initial pressure and thought they had taken the lead in the 25th minute as Jack Diamond fired into the bottom corner, only to be very harshly judged offside by the linesman.
Town did claim the opening goal just four minutes later though, with Thomson the man to break the deadlock on his 200th club appearance.
Lewis Page's delivery was met by Luke Armstrong and fell to Jack Muldoon, who teed up Thomson to smash the ball home.
Town added a second goal ten minutes before the break, again from a full back getting high up the pitch as Fallowfield this time put in a teasing delivery that Byrne could only divert into the back of his own net.
It could have been three for Town in the 39th minute when Armstrong picked out Diamond at the back post, but Jonathan Mitchell made an important save to keep his side in the contest.
Challinor changed things at the break, introducing Gary Liddle and changing his side's system, though Town again had the ball in the net in the opening minutes as Thomson found the net direct from a corner, but the goal was disallowed.
The decision would prove crucial as minutes later Ferguson got forward from wing back to convert Reagan Ogle's cross at the far post and halve his side's deficit.
Within a minute of getting one back Hartlepool were level as Cullen rose above Will Smith to glance Luke Hendrie's floated cross into the corner.
A full turnaround was complete just before the hour mark as Daly netted the pick of the goals, edging past Kerry and bending a left footed shot into the top corner to give his side the lead.
Despite the introductions of Simon Power and Danilo Orsi, Town couldn't get themselves back on level terms and left Victoria Park empty handed.
Town: Oxley, Fallowfield, Page, Falkingham, Smith, Burrell, Thomson, Kerry (Power 63), Muldoon (Orsi 74), Diamond, Armstrong
Subs not used: Martin, Cracknell, Sheron
Goals: Thomson 29, Byrne OG 35
Hartlepool: Mitchell, Sterry (Ogle 33), Hendrie, Byrne, Ferguson, Featherstone, Shelton (Liddle 45), Holohan, Daly, Molyneux, Cullen (Grey 71)
Subs not used: Killip, Jones, Crawford, Fondop
Goals: Ferguson 52, Cullen 53, Daly 59
Referee: S Mather
Attendance: 5,807 (270 away)