The Bees set up a Second Round tie with Stockport County following a come from behind victory away at Bristol Rovers.
The Bees task looked to be a tough one from the outset after only arriving at The Memorial Stadium 45 minutes prior to kick off after getting stuck in traffic.
Perhaps this is the reason for a slow start. Alex Rodman had the ball in the net early on but the cross before hand had gone out of play.
Rodman was allowed to run at goal soon after but his effort from the edge of the box was always curling away from target.
Dan Sweeney had to put in a crucial block from Liam Sercombe's effort before Kyle Bennett's effort from close range struck the post when it looked easier to score.
Michael Kelly fired over the bar before the Bees had their first chance in the 17th minute when Mo Bettamer's header from Elliott Johnson's cross was saved.
Rodman was looking lively for Rovers and forced Mark Cousins in to a smart save, getting down quickly low to his left.
Manny Duku had a chance to play in any of three players on the overlap but instead opted to shoot and his effort went well wide.
There were big calls for a Bristol Rovers penalty have an hour in as Tom Nichols tried to keep the ball in play and collided with Mark Cousins, referee Lee Swabey awarded a goal kick.
Manny Duku was taken off in place of Josh Walker the 35th minute and the Dutchman showed his frustration as he lashed out at the dugout before being sent round to the dressing room.
Cousin's was again called into action just before the break, saving Sercombe's low drive.
The hosts took the lead in the 63rd minute when Bennett brought the ball into the box before delivering a cross on a plate for Tom Nichols to poke home from close range.
Rodman almost added a second as his good effort from distance went just over.
However, the Bees then began to step it up a gear. Walker was unlucky to see his shot deflected before being cleared off the line by a Rovers defender.
The Bees equalised in spectacular circumstances with 76 minutes played. Dan Sparkes cross was cleared out to Sweeney who looped a ball over the defence for Craig Robson to acrobatically lob over the home keeper, more Ibrahimovic than Bees number 6!
Within two minutes, the Bees had completed the turn around with a well worked goal. Cheye Alexander's through ball was backheeled by Jack Taylor in to Walker, he played it wide to Sparkes on the left who delivered a killer ball in and Byron Harrison was there to slide it home and send the 96 travelling Bees fans into delerium.
The Bees then set about shutting up shop, but had Elliott Johnson to thank in the last minute of stoppage time when he cleared Daniel Leadbitter's strike off the line!
The Bees will face Stockport County at The Hive London in the Second Round of the Emirates FA Cup.
Barnet - Mark Cousins (GK), Cheye Alexander, Elliott Johnson, Callum Reynolds, Craig Robson, Charlee Adams, Jack Taylor, Wesley Fonguck (Dan Sparkes, 73'), Dan Sweeney, Immanuelson Duku (Josh Walker, 35'), Mohamed Bettamer (Byron Harrison, 67').
Unused subs - Rihards Matrevics (GK), Shaq Coulthirst, Medy Elito, Ephron Mason-Clark.
Attendance - 2,740 (96 Barnet)