The first half took a while to get going and it was the home side who created the first real chance midway through the half when Max Porter's cross was met by a diving header from Albert Adomah, but unfortunately for the home fans, flashed past the far post.
Gillingham, going down the infamous Underhill slope, grew more threatening as the half wore on and could quite easily gone into the break in front.
A lightning counter-attack saw John Nutter feed the ball out wide to Andy Barcham and as he crossed low into the box, Bees defender Jeremy de Magalhaes, sliding in to clear the danger, skewed his clearance against the bar.
However, they had a much more clear-cut chance to take the lead in first-half stoppage time when Adam Miller dissected the home defence with an inch-perfect slide-rule pass, Simeon Jackson was clean through though with just Rob Beckwith in the home goal to beat, but the latter spread himself superbly to keep the score goalless.
That though didn't prove to be the case for long as within 12 seconds of the restart, Michael Leary ran unchallenged to the edge of the box before unleashing a shot from the edge of the box past Simon Royce.
However, not pushing on from there, the Bees were pegged back in the 67th minute when Barcham struck home at the second attempt, having seen his initial attempt blocked.
Justice, as far as the home supporters were concerned, was restored three minutes later when John O'Flynn headed home Nicky Deverdics' cross.
That seemed as if it would prove good enough for the win, but in a dramatic finish, Barry Fuller's long throw was headed home by Jackson.