Sub Jake Hyde hit the winner with almost the last kick of the match at Underhill this afternoon.
It gave Barnet a third win on the trot.
The game looked to be heading for a draw, until the striker, who had only been on the pitch a couple of minutes, turned to shoot under the visiting keeper after the Magpies had failed to deal with a Paul Furlong cross from the right.
It meant a third clean sheet in a row for Barnet.
In a match of few clear-cut chances, the Bees were good value for what looked like being at least a point, again looking solid at the back.
There was little between the two sides, the Magpies shading the first half in terms of possession, but the hosts taking control after the interval.
It was not the classic most had hoped for, but the Bees can take heart from another promising performance, this time against the title favourites.
Barnet boss Ian Hendon made two changes from the side that beat Torquay on Saturday. Striker John O'Flynn came in for Jake Hyde, while Daniel Leach replaced Clovis Kamdjo in the heart of the defence.
The large County following felt their side should have had a penalty in the fourth minute, Brendan Moloney bursting into the box and hitting the deck under challenge from Ahmed Deen, but nothing was given.
Lee Hughes then saw a long-range effort deflected wide in what was a bright start by the visitors.
Barnet keeper Jake Cole had to turn over another Hughes effort after Karl Hawley had teed up the striker.
The Bees' first shot came from Albert Jarrett, but it lacked power and proved an easy save for Kasper Schmeichel.
It at least gave the hosts something to build on and they gradually got into the match, the Magpies having looked the more threatening in the early exchanges.
County did have the ball in the net ten minutes before the break, Hughes finishing off a flowing move, but the flag had long gone up.
Though the visitors enjoyed the majority of possession in the first half, they never really created a clear-cut chance and the sides went in still on level terms.
Barnet had a great chance to break the deadlock four minutes into the second half, Mark Hughes freeing O'Flynn. The striker had just Schmeichel to beat but shot a foot wide of the post as the keeper came out to narrow the angle. It was the clearest opening either side had carved out.
The Bees started the second half well, and Mark Hughes should have done better from a central position, but scuffed his shot a little and it drifted well wide.
A minute later, Albert Adomah forced Schmeichel to push away a drive, as the Bees kept up the pressure.
At the other end, County struggled to make much progress, continually frustrated by the offside flag.
Sadly, Barnet could not build on their promising start, the second half becoming a rather tame affair.
With eight minutes to go, Cole came out quickly to deny Ricky Ravenhill who had been threaded through by a fine Luke Rodgers pass. It was a great block and kept Barnet in the game.
And, deep into stoppage time, sub Jake Hyde was to win it for the Bees, firing under Schmeichel.
BARNET (4-4-2): Cole; O'Neill, Leach, Deen; Adomah, Hughes, M Hyde, Jarrett (Bolasie 74); O'Flynn (J Hyde 90), Furlong. Subs not used: Carpenter, Devera, Kamdjo, Tabiri, Charles.
Attendance: 2,858.
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