Despite an improved Aylesbury performance, United found themselves hampered by a succession of injury worries and a poor refereeing display as they went out of the Errea Cup.
The first half was a lively affair, in stark contrast to the Stourbridge match, with the Ducks edging the play but finding themselves behind at the interval.
Aylesbury could have scored in the 2nd minute when the excellent Richard Pringle rose highest to meet a Nando Perna free-kick, but his header went over.
In the same incident captain Enzo Silvestri and Barton's goalkeeper collided, and there was a five minute stoppage as both received treatment for head injuries. Despite attempting to come back onto the pitch, Silvestri came off the worst and eventually had to be taken to hospital with suspected concussion.
That meant an early change as Matt Butler came onto the pitch, with Pringle taking over captain's duties.
The next chance fell Barton's way, as a free-kick 25-yards out was blasted through the wall, before being deflected past the post.
Leon Gutzmore was then booked for querying one of the referee's bizarre decisions too strongly.
Pringle threatened again six minutes later when he collected the ball outside the area, made inroads towards goal before firing a left-footed shot wide of the post.
A mistake in the Ducks backline on 21 minutes allowed Barton's rangy striker to be played in, but he wasted the opportunity with a weak shot straight into Tom Vincent's arms.
Some sustained Aylesbury pressure lead to a succession of corner kicks, although the first was the most dangerous as Pringle produced a top drawer header bound for the top corner. Unfortunately he was denied as the home keeper got across to spectacularly tip the ball over; obviously showing no ill effects from the earlier collision with Silvestri.
With half an hour played, Barton took the lead in fortuitous circumstances. The unfortunate Daniel Mead slipped under pressure as the last man, and United could only watch as the ball was played square to Daved and with no defender within 15-yards he easily converted. 1-0 Barton Rovers
Aylesbury looked to respond straight away when another fantastic free-kick from Perna was spilled by the goalkeeper, and from a tight angle Gutzmore couldn't quite turn the ball home and had to settle for a corner.
United did get the equaliser ten minutes later. Another perfect free-kick from Perna picked out Gutzmore, who showed all his quality with a textbook header which dropped in off the post. 1-1
The Ducks pushed on looking for a second before the break, but they were caught out as Barton scored on the counter-attack. A swift move resulted in the ball being worked out to the right, before being crossed low and hard. A half-clearance fell invitingly to Whyte, who steadied himself before lashing the ball home. 2-1 Barton Rovers
Half-time: Barton Rovers 2-1 Aylesbury United
The second half was less eventful, as Barton seemed happy to protect their lead by leaving one man up front for the majority. As well as securing the win, it was a ploy which frustrated the Ducks, as they simply couldn't break down Barton's massed ranks.
When the chances came they were often followed by opposition counter-attacks, and one such example saw Pringle break free, but the defenders caught up with him and instead of shooting he opted to pass infield and the chance was gone.
Then at the other end a punch by Vincent under pressure dropped to a midfielder, but in trying to catch out the Aylesbury stopper he fired well over.
Aylesbury went agonisingly close on the hour mark when Daniel Mead took a free-kick, which curled narrowly wide of the top-right corner.
Then came the best move of the game, although it belonged to the home side. A winger got away down the right, where Vincent came charging out to meet him. His low cross left the goalkeeper stranded, but luckily Kyle Kilmartin was on hand to scramble away the danger.
As the game fizzled out to a close Leon Gutzmore had a great chance to send the match into extra time, but he snatched at his shot from 10-yards after great work from Pringle to get the ball across.
The only final event saw Daniel Mead booked for dissent in the closing stages, and United's Errea Cup campaign was brought to an end for another season.
