Garner’s header settled the issue in front of a bumper crowd of 7,920 - the biggest ever at this level of football - as the Shaymen returned to the Conference at the first time of asking.
Town took the lead on 48 minutes, courtesy of Kevin Roberts’ effort, but a superb free-kick from Adam Blakeman restored parity on the hour mark.
The game was calling out for a hero in the extra half hour and it was Garner, who came up trumps, with the final whistle being the prelude to a joyous pitch invasion from delirious Town fans.
A cagey and tense first-half devoid of action ensued, with chances at a premium.
Halifax, who made one change from the side who eliminated Salford, with Richard Peniket starting ahead of Tom Denton, could only muster a couple of half-chances in front of a very healthy looking crowd.
Just after the half hour, Jordan Sinnott’s long throw wasn’t cleared and fall to Scott Garner, whose effort was comfortably held by Ritchie Branagan.
Shortly before the interval, David Lynch then saw his rising shot fly just over the top after being teed up by Dion Charles.
Chorley produced some decent approach play at times, but failed to trouble home keeper Sam Johnson, whose only significant work saw him gather a low shot from Jack Simpson just before the break.
The Shaymen lost Josh Wilde to injury after 24 minutes, with the left-back feeling the effects of an early challenge, while Magpies defender Stephen Jordan limped off nine minutes before the break.
But after a pretty forgettable first period, the hosts - no doubt cajoled by some choice words of encouragement from Billy Heath - stepped it up on the restart and soon get their reward.
Neat play down the right ended with Sinnott slipping in Roberts with a lovely-weighted pass and he slid the ball under Branagan.
It provided the perfect platform for the Shaymen, who showed signs of settling and they spurned a good chance to make it two just before the hour mark, which proved a big moment.
Sinnott sent Matt Kosylo clear, but he showed a distinct lack of composure in blazing over when well placed and not too long after, the Magpies were level.
Blakeman was brought down in a dangerous position by Nathan Hotte, with the Chorley left-back assuming free-kick duties and firing a sweet precision effort low past Johnson for an exquisite leveller.
The final half-hour became increasingly open, with Marcus Carver just failing to bundle home after a mistake by Johnson, with Tom Denton then firing straight at Branagan at the other end.
Sub Jason Walker soon saw a header held by Johnson before Branagan parried a strike from Sinnott as both sides sought a winner in normal time.
The final chance during six minutes of added-on time saw Johnson grasp Blakeman’s low shot.
Nerves ensued in the extra half hour with Town going close with Sinnott’s well-struck free-kick turned away in textbook fashion by Branagan.
Moments later, the hosts forged a priceless breakthrough when Garner’s smart near post header sailed past Branagan after a cross from right after Sinnott’s long throw wasn’t cleared.
Kosylo spurned two chances to make the game safe in the second period of extra-time, while Chorley goalkeeper went the closest for the visitors, firing a late volley over after supplementing the attack. But it was Halifax’s day.
FC Halifax: Johnson; Roberts, Garner, Brown, Wilde (Denton 24); Lynch (Clarke 79), Hotte; Kosylo, Sinnott, Charles (Moyo 62); Peniket. Substitutes unused: Drench, Morgan.
Chorley: Branagan; Teague, Leather, Jordan (Charnock 37); Challaner, O’Keefe (Walker 59), Whitlam (Roscoe 115), Cottrell, Blakeman; Carver, Sampson. Substitutes unused: Jarvis, Beesley.
Referee: D Middleton.
Attendance: 7,920 (1,941 Chorley).