A filthy afternoon at Nethermoor - swirling wind and constant rain - made it very difficult for both sets of players.
But by the end it was Town who were all washed up and blown off course as Guiseley booked their place in the first round.
Town shaded the opening 45 minutes and should have been ahead but Steve Payne's spot kick was saved by Guiseley keeper Jon Worsnop.
But once James Dean had missed an early second half opportunity it started to unravel and the home side ran out easy winners.
Mark Bett made hay, bagging two goals after James Walshaw had been gifted the first.
Town managed to have a second spot kick saved with 10 minutes remaining but Nicky Gray followed up his own kick to force home the rebound.
James Riley glanced a near post header over the bar in the second minute as the Shaymen opened well.
At the other end, the conditions helped a Dave Merris corner towards goal and Jonathan Hedge was forced to palm the ball clear.
Scott Phelan - the best player on the pitch for much of the game - tried an audacious effort after 18 minutes, beating two players on the halfway line before spotting Worsnop off his line and firing a shot agonisingly wide.
That appeared to inspire Town for a brief spell with Mark Peers racing clear on the left only to be denied by the advancing Worsnop.
And they were handed a great chance to go ahead in the 25th minute when a Tom Baker free kick bounced up and onto the arm of James Cotterill.
The referee pointed straight to the spot and Payne struck his penalty well, but Worsnop dived to his right to push it away.
As much as Phelan's shot had inspired the Shaymen, the penalty miss seemed to deflate them and Guiseley came into the tie.
Danny Lowe blocked a shot from Craig Bentham who also managed to send an effort out for a throw in.
And on the stroke of half time Walshaw got free on the left and went round Hedge but Riley was back to knock the ball clear.
Town had a second gilt-edged chance to open the scoring five minutes after the break when Baker's long range effort was spilled by the keeper.
Gray's rebound was blocked to Dean but he was unable to keep his shot down and the opportunity went.
Hedge got an unconvincing touch to a Cotterill free kick before Town threatened again, Mark Hotte picking out Gray whose shot was saved by Worsnop.
And within 30 seconds Town were made to pay for failing to take any of their opportunities when Walshaw raced down the right, dumped Riley to the floor with a turn onto his left foot and curled home.
Hedge produced a great save on the hour to somehow put a Liam Needham shot over the bar and the keeper saved from Walshaw from the resulting corner with Lowe blocking Bentham's follow up on the line.
There was little respite from the home side's pressure and Guiseley made it 2-0 in the 69th minute from Walshaw's ball up the middle. Hedge called, Hotte left it for him and Bett nipped in between them both to poke home.
Two became three - and game over - nine minutes later as the Town defence was ripped to shreds. A neat passing move involving Steve Burton, Walshaw and Muller ended with Bett steering the ball home.
Phelan tried from distance again soon after and Town managed to pull one back with 10 minutes remaining after Jamie Smith had been bundled over in the box by Danny Ellis.
Gray's spot kick was saved by Worsnop, but the Town man reacted quickly to force home the rebound.
Smith's shot from distance went wide before Bett was denied a hat-trick by a post as he got a flick onto a Walshaw shot that was going wide.
Town finished with a Peers effort that flew straight into the keeper's arms and a Baker long ranger that bounced wide.

MATCH FACTS
Guiseley: Worsnop, Briggs, Merris, Holland (Burton 46), Ellis, Cotterill, Muller, Bentham, Walshaw, Bett, Needham. Subs (not used): Tuck, Singh, Malcher, Askham.
Goals: Walshaw 56, Bett 69, 73
Booked: Briggs (foul 57), Bentham (foul 69).
Sent-off: None

FC Halifax Town: Hedge, Hotte, Lowe, Payne, Riley, Peers, Gray, Phelan, Dean, Baker, Marshall (Smith 62). Subs (not used): Senior, Sanasy, Codman, Sykes.
Goal: Gray 80
Booked: Riley (foul 57), Phelan (foul 69), Baker (unsporting behaviour 78)
Sent-off: None

Attendance: 919
Referee: Mark Ackerman

STAR SHAYMAN
It was never going to be a day for the finer point of the game. The ball skipped off an increasingly slippy surface and when it was played in the air it could have ended up pretty much anywhere.
And that made Scott Phelan's display, especially in the first half, all the more impressive.
He sprayed passes from the middle of the field to both wings and almost scored a spectacular goal after beating two men and showing great vision.
Throw in his tackling stint as well and it was a fine all round effort.
Defensively, Town were found wanting but Danny Lowe continued his comeback from injury with a solid enough display.
He made a couple of important blocks and his distribution was generally good as well.
Phelan takes the three points on offer in our season-long competition with Lowe claiming two while the final one goes to Nicky Gray.
He may have missed his penalty, but he was alive to the rebound and forced the ball home.
It gave Town a glimmer of hope, but no more.

PLAYER POINTS
Gray 23, Marshall 20, Payne 19, Dean 18, Crossley 15, Baker 12, Hedge 10, Riley 8, Phelan 7, Hotte 7, Hardy 6, Codman 4, Lowe 4, Harrison 2, Peers 2, Richardson 2.

YOU SAY
Very poor defending cost us, we need ryan crossley back asap. andy g

Hard luck Shaymen - no shame - more time to concentrate on the league. It won't be easy.
Bri W7

Heartbroken, disappointed and so embarrassed ! The fans turned out in the conditions who else can say that? worried man