Despite a spirited second half comeback, Town were eliminated from the Play-Offs at Mill Farm courtsey of a 3-1 defeat.
Two goals inside the opening 15 minutes had given Town a mountain to climb as Ryan Croasdale and Andy Bond put their side in a great position.
Jack Muldoon was denied from the spot moments before the break, though Luke Burke's own goal gave Town hope of a comeback.
Despite their best efforts, Dan Bradley struck just as the tie entered stoppage time to end any hopes Town had of meeting Solihull in the Semi-Final.
Simon Weaver made two changes from the side that sealed their place in the Play-Offs against Gateshead, with Jack Emmett and Muldoon replacing Lloyd Kerry and Michael Woods.
Croasdale almost gave Town the perfect start after five minutes when he turned Jack Senior's low cross towards his own goal, forcing Jay Lynch into a clever reaction save.
Despite Liam Kitching testing the Fylde stopper three minutes later, it was the hosts who took the lead ten minutes in.
Danny Rowe's corner was headed back into a dangerous area at the far post by Jordan Tunnicliffe, with Croasdale nipping in front of Callum Howe to poke home.
The Coasters doubled their lead five minutes later when Rowe's long range shot swerved in the air before being parried by James Belshaw, only to the feet of Bond who gratefully tapped home.
Town almost pulled a goal back in the same fashion Fylde had opened the scoring, with a set piece routine, but Rowe was in the right place to hook away Howe's header.
With 11 minutes until the break, Fylde had the chance to make it three when a right wing cross found Nick Haughton, but the Fylde attacker could only head wide.
Town then had Belshaw to thank for keeping the score at two as the stopper tipped Dan Bradley's effort destined for the bottom corner round the post.
Weaver's side were given the chance to halve the deficit in first half stoppage time when Jordan Thewlis got round Lynch and was brought down by the Coasters stopper, resulting in Referee Peter Gibbons pointing to the spot.
Former Fylde man Muldoon stepped up, but saw his attempt saved by Lynch as Town entered the break two down.
Town got their goal eight minutes into the second half when half time substitute Joe Leesley's free kick was won by Kitching and went in off the legs of Burke after Thewlis' finish had been blocked.
With only one goal between the sides, Town piled on the pressure and almost levelled on the hour mark when Leesley's corner was a fraction away from finding Beck at the back post.
Fylde remained a threat though, with the introduction of Alex Reid causing Town problems and forcing Belshaw into a good save with his feet to deny the frontman.
With seven minutes of the 90 left, Ryan Fallowfield was dispossessed on the touch line allowing Reid one on one with Belshaw, but Town's stopper came out on top.
It wasn't long before Reid got another chance as Warren Burrell's pass was intercepted on the half way line, though the Fylde man couldn't make it count again as he struck the foot of the post.
Just as four minutes added time was indicated, Bradley fired into the back of the net from outside the area to end Town's hopes of a comeack.
Harrogate Town: Belshaw, Fallowfield, Senior (Leesley 45), Falkingham, Howe, Burrell, Emmett, Beck, Thewlis (Knowles 67), Muldoon (Thomson 75), Kitching
Subs not used: Cracknell, Agnew
Goals: Burke Own Goal 53
AFC Fylde: Lynch, Francis-Angol, Byrne, Tunnicliffe, Bond, Croasdale, Rowe, Philliskirk (Reid 61), Burke, Bradley (Odusina 94), Haughton (Crawford 77)
Subs not used: Hardy, Griffiths
Goals: Croasdale 10, Bond 15, Bradley 90
Referee: P Gibbons