Things started well however and in the fifth minute Dwain Clarke lost his marker and his cross was inadvertently headed into the net by Barking's Terry Scotchmer.
Within minutes Clarke twice created chances for namesake Steve but the veteran striker couldn't quite reach either pass. Kieran Knight then had a great chance in his first start for the Ducks, but his header sailed just over the bar.
Clarke, Knight and Clark all had chances to increase the lead before the home side came back into the game as their best effort of the half crashed off the crossbar, down onto the goal line and clear.
After the break Aylesbury's chances were few and far between as Barking looked to capitalise on another lacklustre Ducks performance. The equaliser came on sixty four minutes when Stuart Moody struck a twenty five yard effort past Adam Wheeler and after that with only a solitary exception there looked only to be one winner.
Gareth Risbridger almost marked his Ducks debut with a goal but his powerful header came back off the bar and from the rebound Knight's overhead kick went wide.
Barking's persistent pressure paid off nine minutes from time when Rob Paris made a rare mistake to allow Dean Allen to cross to an unmarked Jay Murray who made no mistake from five yards, giving his side only their sixth win of the season.