The winner came in controversial circumstances as referee Carl Berry pointed to the spot, having adjudged David Stephens to have handled Sonny Bradley's goal-bound drive.
Craig Reid stepped up and confidently slammed the spot kick past Graham Stack, and things went from bad to worse for the hosts as they were reduced to ten men when Jon Nurse received his marching orders for a dangerous challenge on Dani Lopez.
And Bees boss Edgar Davids was enraged yet further as his men were denied a leveller, with Jake Hyde ruled offside having bundled home Ricky Holmes' near-post centre.
"I think the penalty was harsh. In my opinion, when the ball is that close, he can't really do anything about it. So, his first reaction is get out of the way and that's what he did," said the disappointed Barnet boss.
"The referee said [Jon] went over the top of the ball, if that's so, it's a red card. If not, it was a bad call.
"Hyde's goal was onside. In this particular match you have to be sharp and you see that the standard of the refereeing was not up to the normal level. And it's very disappointing for us that it resulted in a loss.
"I definitely feel that the team was leggy. You already saw that at Exeter. But the fresh legs that came in did ok.
"In the second half we started slowly, and you see that if you're not concentrated anything can happen.
"I would definitely have settled for seven points over Christmas. Christmas was definitely very good for us."