Setanta Shield Jon Shaw's last-minute penalty sent Halifax through to the Northern semi-finals of the Setanta Shield.
The striker fired home after Nuneaton defender Carl Palmer had handled Tom Kearney's corner.
Town's best chance of a goalless first half went to Simon Heslop who surged into the area on the right only to send his shot into the side netting.
At the other end, Palmer fired well over the top from distance and Adam Legzdins saved from Andy Brown's downward header.
Late in the first half home captain Tom Curtis whipped in a free-kick from the left which Legzdins forced behind for a corner.
Halifax dominated the second half and should have gone ahead when Andy Campbell raced clear but he fired wide.
Shaw had an effort cleared off the line midway through the half and Matt Doughty sent a right-foot effort wide.
With time running out Halifax started to turn the screw with Shaw, Heslop and Lewis Killeen all going close before Shaw's dramatic spot-kick winner.
Nuneaton Borough: Acton; Travis, Franklin, Curtis, Moore; Noon, Collins, Palmer, McIlwain; Rodman, Brown. Unused substitutes: Pritchard, Cowan, Williams, Edmond, Nelmes.
Halifax Town: Legzdins; Davies, Doughty, Quinn, Clarke; Kearney, Griffith (Forrest 60), Heslop; Nelthorpe (Campbell 53), Killeen (Wright 90), Shaw. Unused substitutes: Mawson, Whitehouse.
Referee: G Scott.