Chester crashed out of the FA Trophy at the last 16 stage courtesy of Jordan Burrow’s goal for the Shaymen.
The half time scoreline was probably unfair on Chester, but it was the hosts who had the first chance; Ben Heneghan blocking well from McManus who had a chance inside the six yard box.
But the Blues did have plenty of opportunities in the opening half though – Ross Hannah’s first effort was a header which was deflected behind – before Johnny Hunt fired over after good work by Ryan Higgins.
Craig Mahon was then denied by Johnson following a clever short corner routine.
The Shaymen missed a huge chance on the half hour mark – but Peniket missed a glorious chance from close range after connecting with a whipped free kick.
Jordan Chapell certainly impressed in the opening 45, his first shot on target came following a run in which he held off four defenders – before moments later he twisted and turned 25 yards out but could only strike the side netting.
Johnson was then wise to a John Rooney free kick and made a comfortable save – before the hosts took the lead on the stroke of the break.
Former Blue Kingsley James got the flick on – and Jordan Burrow tapped home from close range.
After the interval Hannah was desperate to help the Blues find a way back into the game – but his effort on 51 minutes was off target.
Chapell then smashed one beyond the post – before Jon Worsnop made a superb one-on-one save to deny Peniket a Shay second.
The Blues were running out of time, and were trying desperately to at least clinch a replay – Higgins’ shot going well beyond the crossbar after the ball took a bobble.
Rooney then had a penalty shout turned down – before being brilliantly denied by Johnson from a corner.
FC Halifax: Johnson, Roberts, Brown, Bencherif (Hibbs 27), McManus, James, Wroe, Walker, MacDonald (Hughes 63), Burrow, Peniket (Fairhurst 70).
Subs Not Used: Porter, Miller.
Chester: Worsnop, Higgins, Sharps, Heneghan (Hughes 52), Hunt, Shaw, George (Lloyd 14), Rooney, Chapell, Mahon (Richards 70), Hannah.
Subs Not Used: Thompson, Hobson.
Scorers: Burrow 45+1.
Attendance: 878 (157 Chester).