Notts County edged a tight first half and caused the home side numerous problems from corner kicks.
Barnet's back line struggled to deal with county's extra height especially from midfield. However the Bees should have been in front after eight minutes.
Tresor Kandol pounced on a mix up between Julien Baudet and Nathan Doyle on the edge of the box. The big striker brought the ball under control but could only fire wide with the goal at his mercy.
Kandol was made to pay for his miss as County took the lead almost immediately after the restart.
Steve Scoffham ran onto a precisely weighted through ball from Nathan Doyle before steadying himself and firing an unstoppable low drive across Ross Flitney and into the bottom corner.
Baudet was then fortunate to escape unpunished after he appeared to swing an elbow in the direction of Barry Fuller.
Much to everyone's amazement the referee only awarded a drop ball with the home fans calling for a red card.
Barnet were awarded a penalty on 62 minutes. Anthony Charles' header went into the net but the referee had spotted a hand ball in the melee. Ian Hendon stepped up to cooly fire down the middle with Kevin Pilkington diving to his left.
Ten minutes later the home side were awarded their second spot kick of the afternoon.
David Pipe was harshly judged to have pulled down Andy Hessenthaler and Hendon made no mistake to claim his second goal of the game against his former employers.
Despite a couple of late scares, the Bees held firm to claim three points that could prove so invaluable in their fight against the drop.