Barnet claimed only their second league win at Underhill this season thanks to
Dean Sinclair's first-half penalty.
Chester were made to pay for a Jon Walters miss in the 28th minute Sinclair converted a penalty after he was brought down by Kevin Sandwith.
Barnet were awarded a second penalty when Ismail Yakubu was fouled but John Danby kept out Nicky Bailey's effort.
The visitors finished the game with 10 men after Roberto Martinez was sent off
late on for a second bookable offence.
Barnet: Flitney, Devera, King, Yakubu, Nicolau, Puncheon (Graham 90), Bailey, Hessenthaler, Sinclair, Vieira (Warhurst 76), Kandol.
Subs Not Used: Gross, Cogan, Jaimez-Ruiz.
Booked: Flitney, Kandol, Hessenthaler.
Goals: Sinclair 29 pen.
Chester: Danby, Marples, Westwood, Artell (Linwood 46), Sandwith (Holroyd 73), Bennett, Stephen Vaughan (Bolland 46), Martinez, Wilson, Walters, Blundell.
Subs Not Used: Hessey, Palethorpe.
Sent Off: Martinez (85).
Booked: Martinez, Blundell, Westwood.
Ref: R Lee (Essex).