Dom Knowles 94th minute winner means Town will contest the National League North Play-Off Final next Sunday at The CNG Stadium.
Town had fallen behind through Josh O'Keefe, but Knowles struck from the penalty spot in the second half to level the scores.
With almost the last kick of the game, Josh Falkingham's shot fell to Knowles, who remained calm to slot past Matt Urwin and snatch victory.
Simon Weaver made six changes from last Saturday's 5-0 win over Curzon Ashton, with places on the bench for both Toby Lees and Lloyd Kerry who impressed in that game.
Town made a quick start with George Thomson and Jack Emmett trying their luck from range, before Town struck the woodwork in the eighth minute.
Mark Beck tried to convert Joe Leesley's cross at the back post, but saw his finish kept out and fall to Emmett, who managed to poke into the path of Dom Knowles only for the striker's shot to clatter the cross bar and bounce clear.
Town were playing some easy on the eye football early on and almost went ahead as Knowles' backheel found Ryan Fallowfield on the overlap, whose pull back was hit by Thomson, but deflected wide for a corner.
The lively Emmett went close after the half hour mark, playing a clever one two with Beck to get behind the defence, but Urwin denied the midfielder low to his left.
Seconds later Thomson went within a fraction of finding the goal Town were searching so desperately for, but fired a fraction wide of the far post from a tight angle.
Despite the first half being one way traffic, it was Chorley who snatched the lead nine minutes before the break as Josh O'Keefe converted Alex Newby's low cross from close range.
With a minute to go until the break, Lee Molyneux was shown a straight red card by Referee Rebecca Welch for a high challenge on Ryan Fallowfield on the half way line.
The first chance of the second half fell Town's way as Thomson's corner was headed goalwards by John McCombe, but caught by Urwin.
Just past the hour mark Town were awarded a penalty as Fallowfield's cross was handled on the line allowing Knowles to step up and dispatch the spot kick down the middle to silence the visiting supporters.
Joe Leesley tried to fire his side ahead in the 75th minute after cutting inside on his right foot and shooting, but the winger's attempt flew over the bar.
Not long after his effort Leesley was replaced by Jake Wright, who almost won the tie for Town in the 88th minute as he attacked Thomson's cross, but headed over.
In the final seconds of play, Falkingham's shot fell to Knowles who kept his composure to slot past Urwin and send Town into the National League North Play-Off Final.
Harrogate Town: Belshaw, Fallowfield, Parker, Falkingham, Burrell, McCombe, Thomson, Emmett, Beck, Knowles, Leesley (Wright 80)
Subs not used: Cracknell, Lees, Agnew, Kerry
Goals: Knowles 61 (p), 94
Chorley: Urwin, Challoner, Molyneux, Teague, Leather, Anson (Wilson 68), Newby, O'Keefe, Carver, Walker, (Whitham 57) Cottrell
Subs not used: Gregory, Burgess, Hughes
Goals: O'Keefe 36
Booked: Leather, Anson, O'Keefe, Challoner
Sent off: Molyneux
Referee: R Welch