Having being ahead for 85 minutes, Town were denied their first three points of 2019 after Jonathan Edwards struck in second half stoppage time.
George Thomson's sixth minute opener had looked like it would get Town's year off to a winning start, but the late goal could not be recovered from as the points were shared.
Simon Weaver made four changes from Saturday's defeat to AFC Fylde as George Thomson, Mark Beck, Jack Emmett and Ryan Fallowfield replaced Liam Kitching, Michael Woods, Dom Knowles and Jack Muldoon.
There was also a place in the squad for defender Toby Lees, who had been recalled from his loan spell at Whitby.
Town almost took the lead inside the first ten seconds as Beck closed down a clearance and tried to find the bottom corner, though Sam Johnson stuck out a leg and diverted the finish behind for a corner.
Town did manage to go ahead as early as the sixth minute as Thomson floated the ball over Johnson and into the corner of the net from the right byline.
Thomson almost got his second soon after with a clever flick from Emmett's cross, though Johnson was able to collect the finish.
Halifax did threaten with a couple of long range efforts before the break, though Town ended the half with another sight of goal as the impressive Lloyd Kerry's low shot was blocked.
While Town again enjoyed plenty of possession after the restart, Halifax did pose a threat, shooting into the side netting twice in quick succession as the tie approached the hour mark.
When the hosts got closer to goal, they were met by a number of blocks, first as Fallowfield kept out Dayle Southwell's attempt, before Warren Burrell threw himself at a dangerous looking attempt on goal.
Niall Maher went closest of anyone in blue to equalising with a curling effort from just outside the box, though it looked like Town would hold on to all three points.
That was until stoppage time when Edwards' low shot took multiple deflections on its way into the net, snatching the hosts a point from the jaws of defeat.
Harrogate Town: Belshaw, Fallowfield, Falkingham, Howe, Burrell, Thomson, Emmett, Beck, Leesley (Muldoon 84), Langmead, Kerry
Subs not used: Cracknell, Williams, Lees, Woods
Goals: Thomson 6
Halifax: Johnson, Sellers, Clarke, Brown, Kosylo, Southwell (Edwards 78), Tomlinson, Preston, Ferry, Maher, Hanson
Subs not used: Rowley, Duckworth, Staunton, Odelusi
Goals: Edwards 91
Referee: J Johnson
Attendance: 1,696 (235 away)