Town brushed aside ten man Chester at the Shay to set up an FA Cup fourth qualifying round tie at Conference side Lincoln City.
An early goal from Jon Worthington settled any early nerves the Shaymen may have had, and they were then helped by the dismissal of Chester’s Michael Powell mid-way through the first half after an attempted head butt.
Despite getting a second through Lee Gregory, Town were made to work hard and looked vulnerable when Chester pulled one back with half an hour to go.
But Chris Worsley’s smart finish after a lung bursting run down the right proved enough as Town sealed a place in the fourth qualifying round for the fourth year in a row.
Neil Aspin named the same side which drew in Chester on Saturday, and Town made a dream start to game when Ryan Toulson’s long throw from the right was only flicked as far as full-back Jason St Juste, whose low cross was stabbed home by Worthington for the midfielder’s fifth goal of the season.
Cheter, who had a chance in the second minute after Danny Lowe was dispossessed, could have levelled straight away but defender Dom Collins couldn’t control after a corner eventually found him unmarked in the box.
After that Town started to turn the crew, and Chester stopper John Danby was booked after he brought down a surging Gregory to the right of the penalty area.
Gregory was involved again a minute later, holding off his defender before picking out Liam Hogan, who had stayed forward following the free-kick, but the defender’s side foot effort was straight at Danby from 10 yards.
Chester began to get a foothold in the game the longer the half went on, although Marc Williams wasted a decent chance when he blazed high and wide from 20 yards as Chester broke.
Then a moment of controversy. As Matt Glennon prepared to take a goal kick, the referee summoned Chester’s Michael Powell towards him and issued a straight red card - thought to be for an attempted head butt on St Juste.
But despite having only ten men Chester continued to push forward, and Nathan Jarman’s delightful dink over Glennon was ruled out for offside ten minutes before half time, and the striker was caught offside again a minute later as he powered a header on target.
It proved to be the final meaningful moment of the half - but Chester boss Neil Young confronted referee Martin Coy on the pitch as the players made their way into the tunnel.
The second half started the same way the first ended with Jarman testing Glennon who gathered on the second attempt after a low drive from the lively striker,
Gregory saw a low effort saved unconvincingly by Danby as Town tried to make the pitch as wide as possible to try against the ten men, and it soon paid dividends.
Lowe’s long ball over the top picked out the run of Johnson, who held off his man before squaring for his strike partner Gregory to round the keeper and lift Town into a 2-0 lead.
The visitors tried to muster a response, Iain Howard’s volley on the turn sailed high above Glennon’s goal.
Town’s keeper had to be at his best to keep out Antoni Sarcevic’s thumping strike from just inside the area and had Toulson to thank as he hacked off the line a minute later.
But the visitors pressure finally told, and just seconds after Howard saw appeals for a penalty waved away after he went down under a Lowe challenge, Marc Williams fired in from close range to reduce the deficit.
Chester looked the side more likely to score next but were caught by a Town sucker punch - Chris Worsley racing down the right before calmly stroking the ball home at the near post after a clever flick from Johnson, for which Collins was later booked,
Substitutes Simon Hackney and Gareth Seddon both put chances wide shortly after coming on as Town looked to finish off their Conference North rivals and Gregory almost had a second when his clever chip just missed the far post.
Seddon thought he had scored a fourth late on only to be denied by the linesman’s flag as Town sealed their place in the fourth qualifying round.
FC Halifax Town: Glennon, Toulson, St Juste (McManus, 46 mins), Hogan, Jarrett, Lowe, Worsley, Marshall (Hackney, 59 mins), Johnson (Seddon, 72 mins), Gregory, Worthington. Unused subs: Senior, Bolland, Qualter.
Chester FC: Danby, Powell, Howard (Williams, 80 mins), Horan (Mankin, 83 mins), Collins, Brown, Hankin, Sarcevic, Jarman (Gray, 78 mins), Williams, Clancy. Unused subs: Fearon, Booth, Ormrod.
Goals: Worthington (5) Gregory (52) Williams (59) Worsley (65)
Off: Powell (30)