Forest Green Rovers had overtaken Town after last night's draw with Aldershot Town, but goals from Richard Peniket, Scott Boden and Matty Pearson ensured that their team continued to be the early pacesetters.
Halifax were in charge of the contest from the opening minute, with Peniket wasting a clear opportunity from 12 yards before Boden had a goal correctly ruled out for a foul.
The Shaymen deservedly took the lead on 35 minutes when Peniket received the ball on the edge of the area before curling his effort into the far corner from 20 yards.
Chester returned for the second half on the front foot, but, after seeing an appeal for handball in the penalty area turned down, Sean McConville drove the ball wide from 18 yards.
Their positivity ended in the 70th minute, though, as Halifax doubled their advantage through Boden, who created some space for himself in the Chester penalty area before heading past Freddy Hall.
The result was put beyond doubt with seven minutes remaining when Pearson raced clear of the Chester defence to drive home a clinical finish to take his team two points clear at the top of the table.