Niall McGinn struck 14 minutes from time to give the visitors the spoils as they moved level on points with Hibs, with both clubs just a solitary point behind leaders Celtic.
The home side were the better team throughout, with Craig Brown making a half-time tactical shuffle to try and shift the attacking flow in Aberdeen's favour.
It may not have had the desired effect on the overall play, where Hibernian were still superior, but provided his team with the ammunition they required to take all three points.
The club's growing injury list saw Ryan Fraser and Gavin Rae miss the game after both were substituted in last week's defeat at Celtic. The victory was indebted to the experienced players, such as Russell Anderson and McGinn, who were available for selection and put in outstanding performances.
Sticking with the recent 3-4-3 system the away side had the first real chance with Cammy Smith dispossessing Paul Hanlon and racing through. Indecisiveness from the youngster allowed Alan Maybury to recover and block the shot.
Leigh Griffiths displayed his usual energy and determination but Aberdeen's back three were clearly under instructions to limit the striker's space in the final third.
The attention toward Hibernian's attacking focal point did grant Eoin Doyle extra room in which to manoeuvre and the Irishman almost opened the scoring on 31 minutes.
Latching onto a through ball in the centre Doyle struck a sweet early shot across Jamie Langfield but the keeper pulled off an excellent save to finger-tip the effort round the post.
With his confidence soaring it was always going to be a difficult task completely shutting down Griffiths. The striker responded to the tactical restrictions by dropping deep in which to find a sight at goal.
After 38 minutes he forced Langfield into parrying away a curling effort from the right corner of the box before skipping past Vernon and driving a lot shot straight at the keeper from a similar angle three minutes later.
At half-time Brown withdrew Smith and replaced him with Rory Fallon. The substitution initiated a switch of system with the 3-4-3 dropped for a very attack orientated 4-4-2.
The change allowed Griffiths greater freedom and the striker had three chances in the first 13 minutes following the break.
First, a close range overhead kick was palmed away by Langfield for a corner before the keeper got down low to push away a low drive from the edge of the penalty area.
Shortly afterwards Griffiths burst into the box again but uncharacteristically dragged his shot wide of the far post.
The away side were struggling to get a foothold in the game with both Vernon and Fallon failing to establish possession in Hibs' territory. However, with such attacking arsenal they were always going to be capable of producing something out of nothing, with Hibs receiving such a warning on 61 minutes.
Andrew Considine, having shifted to left-back for the second half, sent in a deep cross which the defence missed and travelled all the way to the incoming Fallon at the back post. The striker seemed set to score but did not time his jump properly and saw his header from four yards drift over the crossbar.
The match winner arrived 15 minutes later. Hayes' cross from the left took a little touch off Alan Maybury trying to clear. The deflection was enough to take the ball away from the waiting Fallon but dropped into the path of McGinn.
The attacker took a couple of excellent short touches to move himself into a one-on-one situation with Ben Williams before coolly rolling the ball past the Hibs goalkeeper.