The Shaymen had matched their Unibond Premier Division hosts for the first 45 minutes, even taking the lead through Peter Moore.
But, not for the first time this season, they failed to show up in the second period and that allowed Nantwich to coast through to the third qualifying round.
Town played some good football before the break, passing well, finding plenty of space to work in and creating chances.
But it was a completely different story in the second period when Town visibly wilted in the Cheshire sun and managed just a couple of efforts on goal - both Steve Payne headers from Jonathan Smith deliveries.
Halifax opened the game brightly with Paul Gedman holding the ball up well before setting up Smith whose shot from distance was comfortably saved.
Moments late Glyn Blackhurst's cross picked out Dave Walker whose shot on the turn was saved well by Jon Kennedy who also collected Phil Parkinson's long range effort.
Halifax broke the deadlock after 10 minutes following a sublime move down the centre of the field.
Smith flicked the ball on for Gedman whose header helped it into the path of Pete Moore and the midfielder picked his spot from 15 yards to beat Lee Jones.
Ashley Stott almost got away moments later and Cavell Coo sent a volley from Smith's deep cross from the left across the face of goal and wide.
But Nantwich levelled after 16 minutes when Walker turned a Phil Parkinson pass round the corner for Alan Naggington who slid the ball home.
Gedman was unable to direct his header from Steve Payne's long throw goalwards and when Nantwich broke forward Naggington was denied a second by Kennedy's feet.
Coo cleared an Adam Beasley free kick before Michael Lennon found Tickle who whipped a cross across the face of goal from the left.
But Town finished the half strongly with Payne rising well to meet a Smith free kick but heading wide and Nigel Jemson sending a downward header from a Kris King into the arms of home keeper Jones.
There was a warning for Town early in the second half when Michael Lennon found Tickle on the left and he whipped a cross across the edge of the six-yard box.
And, after the first of Payne's headers over the top, Parkinson picked out Naggington after a great run and only a last-ditch block from Payne denied the first half scorer a second.
There was a let off when the ball appeared to strike Lincoln Adams on the arm from a corner in the 55th minute, but within a couple of minutes Nantwich were in front, from another corner that Glyn Blackhurst headed home unmarked.
Payne headed over again just past the hour mark, but it was a rare Halifax threat.
And the game was effectively settled in the 66th minute when Adams dived in rashly on Lennon in the area and the referee had no option but to point to the spot.
Walker stepped up, after a brief injury delay, to send Kennedy the wrong way.
Naggington ought to have bagged his second of the game five minutes later when he latched onto a Blackhurst pass and rounded Kennedy, but he could only fire wide of a gaping goal.
Blackhurst blazed over and Liam Shotton's trickery in the area ended with a well struck shot that Kennedy saved at point blank range.
But the pressure finally told with five minutes remaining when Shotton nodded on a long through ball for Walker who fired home from 12 yards.

MATCH FACTS
Nantwich Town: Jones, Taylor (Smith 46), Tickle, Tinson, O'Loughlin, Parkinson, Beasley, Blackhurst, Walker, Lennon (Shotton 71), Naggington (Griggs 77). Subs (not used): Carter, Gibson, Arestidon, Hawthorne.
Booked: Taylor (foul 39), Walker (foul 54). Sent-off: None
Goals: Naggington 16, Blackhurst 57, Walker 66pen, 85

FC Halifax Town: Kennedy, Coo, King (Ellis 64), Barras, Payne, Adams, J Smith, Moore, Walker (Phelan 64), Gedman (Jemson 37), Stott. Subs (not used): Senior, C. Smith, Morning, Davidson.
Booked: Adams (foul 22), Jemson (foul 78). Sent-off: None
Goals: Moore 10

Attendance: 1,091. Referee: R Newman.

STAR SHAYMAN
Jonathan Smith enjoyed the freedom of the Weaver Stadium pitch in the first half of the FA Cup second qualifying round clash with Nantwich.
And he used it to good effect as he set up several chances for the Shaymen who matched their division higher hosts stride for stride.
He had a hand in the goal, had a couple of shots himself and his delivery from set pieces was spot on.
Alongside Smith in midfield, Peter Moore had another fine game before the Shaymen subsided.
He passed the ball confidently, tackled hard and he took his goal coolly after being sent into the area following a Smith flick and Paul Gedman header.
If there was anyone who did not deserve to lose 4-1 it was keeper Jon Kennedy.
He was left cruelly exposed for three of the goals, including the penalty, yet still came out of the tie with plenty of credit.
He made a couple of very good saves in each half, unfortunately just to keep the score down.
Smith takes the three points on offer in our season-long competition with Moore taking two and Kennedy one.

PLAYER POINTS
Jonathan Smith 13, Paul Gedman 8, Peter Moore 8, Junior Brown 7, Ashley Stott 5, Adam Morning 4, Jon Kennedy 4, Steve Payne 3, Lincoln Adams 3, Cavell Coo 3, Nigel Jemson 2, Craig Smith 2, Justin Walker 2, Phil Senior 1, Luke Hinsley 1.

YOU SAY
half price admission for half a game, lost gedman lost the plot wheres the rest of the game plan embarrassing truth be told ya loosing even the diehards and im 1 of em bye - REALIST

Appalling 2nd. Midfield non exsistant.We are not as good as you think we are Mr Vince! Still 3 or 4 players short - TOWN FAN