Town were denied an FA Cup first round tie against League One Walsall after they were dumped out by Lincoln City.
Town were made to pay for a slow start when they fell behind to Jake Sheridan’s early side footed finish.
Despite seeing more of the ball as the game went on, Town never really tested Imps keeper Paul Farman, apart from a low Gareth Seddon effort early in the second half, and had their misery compounded with just over ten minutes to go after a rare mistake by Danny Lowe allowed Jamie Taylor an easy tap in.
The major positive on a night when there were few was a first appearance on the substitute’s bench for midfielder Dan Gardner, who is yet to play so far this season after damaging his knee ligaments in pre-season.
Neil Aspin named the same side which drew at Sincil Bank on Saturday, but with two additions on the bench as Conor Qualter, who returned after illness, was named alongside Gardner.
The first chance went to the Shaymen, but Lee Gregory was unable to direct his header on target after Ryan Toulson’s near post cross, and on ten minutes Liam Hogan had to be in the right place to clear Alan Power’s effort, but the visitors didn’t have to wait long for the lead.
A minute later Adam Smith’s wonderful curling cross from the right picked out Jake Sheridan who side footed into the bottom corner for 1-0.
Town looked rattled as the Imps dominated possession on the edge of the Town area, with Phil Bolland making some vital clearances as the Conference Premier side looked to press home their advantage.
But Town weathered the early storm and then began asking some question of their own.
First Andrew Boyce was fortunate to get away with some ropey defending after being out muscled by Gregory, and then Paul Farman had to scramble across his goal to keep out Jon Worthington’s deflected drive from 25 yards.
There was a short injury concern on the half hour when Seddon went down holding his knee as he attempted to chase down Boyce, but after some treatment on the sidelines he was able to continue - though his first involvement was to give away possession and then a free-kick, which Danny Lowe was eventually able to clear.
Worsley saw a long range shot charged down as the Shaymen continued to press forward in search of an equaliser but had to settle for going in behind at the break.
As in the first half, Lincoln started the second half brighter and Boyce was unlucky to see his header go wide after an early corner from the left.
Town responded though and both Gregory and Worsley saw long range efforts blocked by defender, before their best chance of the game until then - Seddon’s near post effort beaten away by Farman after good link up between Worsley and Worthington.
Seddon then saw a half chance deflected wide for a corner after a good cross by Lowe, but Town were unable to make anything of it.
Jason St Juste replaced Scott McManus, the man who took his place in the side on Saturday, with 20 minutes to go as Aspin tried to inject some fresh legs into Town’s tiring attack - but in his first venture forward he was immediately surrounded by three City defenders.
But the game was put out of the Shaymen’s reach with just over 15 minutes to go when Danny Lowe’s horribly under hit back pass was intercepted by Mo Fofana, who squared for the unmarked Jamie Taylor to fire into an empty net.
Substitute Colin Larkin then rattled the outside of the post as Lincoln threatened a third almost immediately afterwards, but Town were unable to muster any kind of fightback, and needed a last ditch Hogan tackle to stop Vadaine Oliver making it three in injury time, as the Imps sealed their place in round one.
The Shaymen travel to Conference North leaders Brackley Town on Saturday and will be bolstered by the return from suspension of midfield enforcer Jason Jarrett, who they sorely missed over the course of both games against Lincoln.
FC Halifax Town: Glennon, Toulson, McManus (St Juste, 70 mins), Hogan, Bolland, Lowe, Worsley, Marshall, Worthington, Gregory, Seddon: Unused subs: Senior, Qualter, Hackney, Gardner.
Lincoln City: Farman, Mills, Boyce, Smith (Larkin, 57 mins), Power, Taylor (Oliver, 80 mins), Sheridan, Bore, (Robson, 13 mins) Miller, Nutter, Fofana. Unused subs: Grey, Nicolau, Hutchinson, Turner.
Goals: Sheridan (10) (Taylor 78)