The opening 20 minutes were largely uneventful, with the only pressure being applied at the Paxton Road end that was being defended by Chester. Danny Rose and Andros Townsend were responsible for the early promptings, although the final delivery failed to carve out any openings for Alex Olsen in attack.
A cross from Adam Smith came close to picking out Townsend before James Butler was forced into spectacular action to deny Chester taking the lead. A low cross from Lloyd Ellams sat up for Kieran Morrin, who struck first time and Butler responded with a reaction tip over the bar.
The lead was taken in the 28th minute when a Paul McManus cross was steered into the net by the head of Ellams.
The boys sought a quick leveller and a Townsend centre was zipped over the bar by Jake Livermore. There was then a scramble in front of goal following a Townsend shot and Olsen just failed to latch on to the loose ball.
Townsend was the principal threat and he flashed a drive across goal ten minutes before the break, but we did not have to wait much longer - 38 minutes on the clock.
A drilled Smith cross from the right fizzed across goal and waiting to apply a thumping finish at the far post was Rose.
A lead came close to being registered early in the second half when a Yuri Berchiche cross was nodded goalwards by David Hutton, but a last-gasp block led to an appeal for handball which fell on deaf ears. Another Berchiche cross was headed just wide by Townsend.
Dominance was clearly established in the second period and a second goal seemed only a matter of time. Rose left his marker standing on the hour and fired across goal for Olsen, but the Norwegian striker could not quite propel himself forward enough, while the flag saw to it that it didn't matter anyway.
A Gio Feliciello free-kick again bought out the best in Butler on 64 minutes, the goalkeeper reaching high to divert over the bar.
Coach Alex Inglethorpe replaced Olsen with Jonathan Obika with 16 minutes remaining, but it was Chester who seemed to be taking heart from still being in it in the closing stages.
The turning point came three minutes from time when Rose chased down a Ryan Mason throughball and the goalkeeper, Paul Dorman, appeared to get to the ball first, but the referee thought differently and pointed to the spot.
Hutton stepped up, struck right, and the boys are now in round five.
A David Hutton penalty three minutes from time proved to be the decisive strike as Chester City were defeated 2-1 in the 4th round of the FA Youth Cup at the Lane.It was a tough call on City, who were very much still in the game in the final stages and they were left totally deflated when Hutton cooly dispatched his kick.