When the sides met on Boxing Day, Gary Roberts netted a 90th-minute equaliser to earn the Conference leaders a 2-2 draw.
In the rematch Halifax were 10 minutes away from securing the points until conceding a penalty. Steve Haslam was adjudged to have brought down Roberts and substitute Peter Cavanagh scored from the spot.
Cavanagh had only been on the field for five minutes and his third goal of the campaign was his first since late September.
Despite dropping four points from their two holiday fixtures, Accrington remain three points clear of Exeter and still unbeaten in the league since the November 12.
Halifax are one of the sides chasing Stanley and will feel they deserve to be closer after again throwing away a winning lead.
In an entertaining but physical clash seven players were cautioned, including former Accrington winger Rory Prendergast.
In fact, Prendergast, on loan from Blackpool, was yellow carded in both games between the clubs.
It was another Halifax loan star, Danny Forrester, that put the Yorkshire side in front.
The Bradford City youngster broke the deadlock in the 58th minute, shooting home from 18 yards to register his fifth goal of the season.
Forrest had an opportunity to put the visitors ahead earlier in the game while Roberts and Ian Craney went close for John Coleman's team, before they finally hit the target through Cavanagh's spot-kick.
A draw was just about the right result and leaves Stanley well poised to reclaim their league status going into the new year.