Barnet bounced back from their 5-0 home loss to Lincoln to claim a place in the Johnstone's Paint Trophy second round.
Tresor Kandol's 17th-minute goal proved decisive, but County would have been trounced but for some fine saves by second-string goalkeeper Saul Deeney.
Kandol had a touch of good fortune as Ismail Yakubu's fierce shot rebounded off the bar, hit him and found the net.
The hosts only came close once, when Ross Flitney saved from Tcham N'Toya's point-blank header.
Notts County: Deeney, Silk (Gleeson 80), White, Hunt, Needham, Mendes (Sheridan 59), Somner, Martin, Ross, Dudfield (Akers 62), N'Toya.
Subs Not Used: Pilkington, McCann.
Barnet: Flitney, Devera, Charles, Yakubu, Nicolau, Sinclair, Bailey, Hessenthaler, Puncheon, Kandol, Vieira (Hatch 87).
Subs Not Used: Janiez-Ruin, Graham, Warhurst, Cogan.
Goals: Kandol 16.
Ref: J Moss (West Yorkshire).