United could have taken an early lead though, wasting too good opportunities inside 15 minutes. First Drew Roberts saw his shot well blocked by goalkeeper Tony Kessell having been played in by Jamie Kearns.
Kessell then did well again, Dean Powles the provider this time with a superb pass to pick out Gavin Jaggard, but Kessell was able to block.
Folkestone regrouped and duly struck back, in lethal style. Greg Williams was shrugged off the ball by Paul Jones in the area, and as the ball was cut back hotshot James Dryden couldn't miss from six-yards. 1-0 Folkestone
The goal took the momentum out of Aylesbury's play, and although Kearns threatened with a chipped effort, there was little end product for United.
Jaggard and Roberts too often found themselves starved of the ball - the latter frequently having to drop deep in order to gain possession, leaving his strike partner isolated up front with three defenders for company.
Dryden threatened again with a fierce shot, but it was at a comfortable height for Jack Rashid to confidently catch. Aylesbury's Powles fired a shot over after a free-kick had dropped to him.
The visitors had the last effort of the half, James Everitt drilling in a low effort which had to be tipped wide by Rashid.
Half-time: Aylesbury 0-1 Folkestone
Folkestone continued in the same vein after the interval, Dryden proving to be a real handful for United's defence. He forced Rashid to make a diving save having beaten his man and shot for goal.
Stuart Myall then went close having run though, but his eventual shot went wide. The midfield man came closer still two minutes later, cutting the ball onto his left-foot before smacking the crossbar with a powerful shot.
Danny Nicholls replaced Scott McCafferty with playmaker Jonathan Bewers to try and inject some life into Aylesbury five minutes into the second period. His hand was forced soon afterwards, Dean Powles being caught in the face by an opponent's arm and having to be substituted for Neil Lazarus.
United created their first meaningful chance of the second half after 65 minutes. Paul Edgeworth rounded off a neat team move with a half-volley that had to be tipped over by Kessell.
Roberts found himself clean through and went down looking for a penalty which was waved away by Mr Fay, before Dryden shot wide at the other end.
United had another chance when Kearns went clean through, but his marker did well to recover and assert enough pressure to force the former Kettering midfielder to rush his shot and shoot straight at Kessell.
Folkestone launched a swift counter-attack, and Myall should really have done better when he was presented with an inviting cross, but fired wide of the post.
Jaggard produced a fine piece of skill for Aylesbury when he took the ball past a defender and into the box, but his shot was across the face of goal rather than on target.
With Danny Nicholls preparing to throw on Roni Joe for one last push, Folkestone got the goal they needed to kill the tie. A cross from Dryden appeared to have been touched home by Myall, but indeed the midfielder didn't make contact, and Dryden netted his second of the game, and surely his most important goals of the season. 2-0 Folkestone
Joe did get onto the pitch, replacing Kearns, but the game was over and the result was sealed. Folkestone had got the score they deserved, and were rewarded with a trip to Chester City in the First Round, whilst Aylesbury were left to reflect on what might have been.