Two goals in a minute were enough as Chester held out to earn three valuable points.
Striker Michael Branch produced a masterclass in finishing with two clinical first-half strikes to set up the narrow victory.
The home side were on the back foot for the majority of the second-half, but resolute defending ensured Chester's unbeaten run was stretched to nine games.
Chester had been unfortunate not to take the lead after only six minutes when a lay-off fell to the in-rushing Ben Davies whose left-foot strike cannoned back off the bar.
The home side were not having things all their own way, and Dean Gordon was only inches away with a thunderous strike from 30 yards out.
Chester's persistence was rewarded with two goals in a minute from Branch.
First, on 39 minutes, the striker found the bottom corner with a precision strike from just inside the box after being found by Cortez Belle.
Almost immediately the lead was doubled as Branch robbed the ball from Terrell Forbes, before cooly chipping the ball over the out-rushing Tony Williams.
The visitors, who had not really been in the game, gave themselves a life-line deep into first-half added time as Jon Daly's goal-bound strike took a deflection off Phil Bolland sending it past Chester keeper Chris MacKenzie.
The inevitable early second-half pressure came from the visitors and former Tranmere player Andy Parkinson and Daly both went close, but the home defence remained firm to earn the points.