On-loan striker Danny Crow scored the only goal of the game to secure Notts County's first away win since November.
The winner came after 69 minutes when Ali Gibb delivered a great cross from the right flank which Crow superbly directed past goalkeeper John Danby,
Crow, on loan from Peterborough, had earlier spurned a great chance when he side-footed wide from just six yards.
The nearest Chester came to a goal was a deflected Craig Lindfield effort which hit the top of the crossbar.
Chester: Danby, Vaughan, Butler, Linwood, Wilson (Sandwith 57), Partridge, Dinning, Hughes (Rutherford 83), Roberts, Murphy, Lindfield (Holroyd 60).
Subs Not Used: Palethorpe, Grant.
Notts County: Pilkington, Canoville, Tann, Edwards, Mayo, Gibb, Butcher, Smith (Silk 81), Weston, Jarvis (Weir-Daley 84), Crow (Lee 74).
Subs Not Used: McCann, MacKenzie.
Goals: Crow 69.
Ref: Andy Woolmer (Northamptonshire).