Chester began the game well putting the Town defence under early pressure, Dalton and Spearritt stood firm denying any clear goal scoring chances.
Town competed well in midfield, working hard to gain a share of possession of the ball, the Chester defence was equally in control of play.
When Potter pulled a hamstring after 10mins Town were forced to reshuffle introducing Jason McShane in an unfamiliar fullback role.
It became a midfield struggle with Chester just having the edge, a shot by Menagh was charged down by Wills the loose ball been hacked away by Dalton.
A through ball by Burton put Breen clear but the striker was unable to control the ball as Danby came out and it went out of play for a goal kick.
A header by Dalton back to Wills lacked pace and was seized on by Reed, Wills reacted quickly to block the lively Chester forward.
Reed on the edge of the Town penalty area controlled the ball facing his own goal before turning to hit a fierce shot over the crossbar.
Just as it seemed like a goal less 1st half, the game took a decisive double twist in the 43rd and 44th minutes.
Wills racing from his goal blocked a through ball, the ball fell to Menagh who cleverly played it to John Rooney who clipped it into the empty net.
Within a minute Peers wide on the right took a dive as Wills came out, the Referee awarded a penalty with Wills protesting he had not touched the player.
The supporters in the immediate area disputed the decision compounded by the linesman not supporting the official and no card for Wills.
John Rooney dispatched the penalty to put Chester in control of the game and make a mockery of Town's hard work during the 1st half.
The second half followed a similar pattern to the 1st, Chester playing some excellent football and Town responding with impressive effort and team work.
In the 52min a hard low shot from Williams brought a superb full length save from Wills but the ball fell to Jamie Reed who tapped the ball home.
Danny Salt in charge of Town tonight introduced Duckworth and Edwards on the hour and Town earned a good share of the ball, Dolan standing out in midfield.
As Town mounted a series of attacks on the Chester goal Horan and Kay defended well making it a fairly easy night for their keeper Danby.
Breen beat Danby to a through ball but was unable to get enough power on the chipped ball and Horan comfortably completed the clearance.
From a Haughton corner Dalton headed goal wards but again the ball lacked enough power to trouble Danby.
At the other end from a corner on the right a powerful header from McInyre flew wide of the target.
A long range shot from Jason McShane produced a diving save from Danby. Chester were playing well but Town never gave up and fitness never became an issue.
Wills did well to hold on to a shot from Rooney then even better when he tipped a Miller shot over the crossbar.
In the final minute John Rooney sealed the Chester victory to complete his hat trick with a powerful shot that deceived Wills and found the top corner.