Rune Lange had given the visitors an early lead. But it lasted only seconds as Gerba fired in a equaliser within a minute.
Dons had all the pressure after that but just couldn't seem to find a way past the Hartlepool defence.
Then as the game seemed destined for a draw the skipper popped up for his second of the season. His first was in the corresponding fixture.
It was a win the Dons deserved as after a slow start they were the better team. There was little in the way of clear chances in the first-half as both teams peppered their opponents goal with long shots.
The visitors' Ritchie Humphreys had a good opportunity early on with a free-kick on the very edge of the box but he smashed his effort into the wall.
In reply Gerba's audacious scissor-kick floated miles over the bar.
Sam Baldock then sliced wide before Andy Monkhouse hit a poor shot when presented with time and space down the left.
With neither team creating much it looked like it might take an error to fashion a decent chance and that is what happened.
Alan Navarro played a blind header towards his own goal, Lange, who was returning back up the pitch couldn't believe his luck and in a one-on-one with Willy Gueret, he delicately chipped over the keeper.
Dons' response couldn't have been quicker as Jemal Johnson then raced down the left and sent over a cross that Luke Chadwick miscued, fortunately Gerba was in the right place at the right time and smashed home.
It woke Dons up and they had several decent chances to take a lead into the break after that. Firstly the menacing Jason Puncheon just curled wide with a long range effort. Then skipper Dean Lewington had a shot tipped wide after superb work from Chadwick.
Dons took that momentum into the second-half and Chadwick played a lovely one-two with Johnson but his resulting left-foot shot was weak and straight at Arron Lee-Barrett.
Dons were the ones having all of the ball as they kept the visitors stuck in their own half. They were limited to long-range efforts though, Puncheon firing over then Chadwick shooting at Lee-Barrett.
Eventually a clear-cut chance came as Lewington played a lovely ball in behind the defence for Baldock who tried to slot the ball under the keeper who just got a touch on the ball to send it wide.
In their search for a goal Dons brought on Peter Leven and Tore Andre Flo. But instead of inspiring the Dons they seemed to lose their momentum a tad.
They struggled to create chances after that and it looked like a goal wasn't going to come. Then with four minutes left the Cow Shed erupted as its darling found a winner.
Johnson beat his man again down the left and his cross found the head of captain Lewington who on a rare gallivanting run up the pitch hit a lovely glancing header that trickled in at the far post.
The skipper enjoyed his moment in front of the Dons' fans and raced towards them to celebrate.
Then to rub salt in the wounds late on the Dons added a third.
Flo was played through on goal and unselfishly squared for Gerba who smashed into the empty net.