Dons boss Jimmy Calderwood will feel that his side had been mugged as they dominated proceedings for much of the game.
However, they failed to put away several clear-cut chances, with man of the match Yves Makaba-Makalamby producing a heroic performance in the visitors' goal as he thwarted the home side on numerous occasions.
Hibs boss Mixu Paatelainen won't be bothered too much about his side's performance since they picked up their second consecutive victory on the road.
He will be particularly pleased with the resolute performances of skipper Rob Jones and Souleymane Bamba.
The first opening came on six minutes. Steven Fletcher cleverly turned away from Alexander Diamond on the left, but his deft ball into the area was cleared by Lee Mair with Colin Nish looking to cash in.
Aberdeen ought to have gone ahead on 15 minutes. A tremendous throughball from Darren Mackie saw Richard Foster race clear on goal. The midfielder's attempt to bend the ball beyond the advancing Makalamby ended with the big keeper brilliantly palming the ball away.
On 19 minutes Fletcher created a great chance for his strike partner Nish. Nish advanced to the edge of the area but his shot from 18 yards screwed well wide of the target.
At the other end minutes later Lee Miller headed on to Darren Mackie who chested the ball down before firing in a fierce left-foot volley which Makaba-Makalamby got down well to hold.
The visitors' Lewis Stevenson did brilliantly to get beyond Jared Hodgkiss, the youngster cleverly pulling the ball back into the path of Derek Riordan whose first touch took him away from Mark Kerr, before smashing in a left-foot shot which flew across the goalmouth.
The home side threatened at the Richard Donald end. Sone Aluko fed the ball to Miller who crashed in a great shot which was again well held by Makaba-Makalamby.
The visitors shocked the Dons on 32 minutes by taking the lead. Mair should have cleared but he hesitated allowing Fletcher to nick the ball away from him. He set up Riordan who easily rounded Jamie Langfield before slotting the ball home.
Aberdeen were given a chance to get back on terms on 41 minutes. Kerr fed the ball through to Miller who was bundled over inside the area by visiting skipper Rob Jones. The striker accepted the responsibility by coolly slotting home the resultant penalty.
Aberdeen had taken great confidence from their goal and almost took the lead on 44 minutes. Miller played the ball off to Kerr whose crisp shot from 20 yards was just wide of the upright.
Aberdeen continued to dominate the start of the second half as they swarmed all over the visitors. A shot from Kerr was charged down by David van Zanten on 56 minutes, the ball breaking to Charlie Mulgrew whose flashing effort went narrowly wide.
Dons midfielder Richard Foster made a telling run into the visitors box driving past three defenders before being foiled by Makaba-Makalamby who bravely saved at his feet.
Hibs' first serious attack of the half on 75 minutes almost brought the visitors an unlikely lead. A deep ball from John Rankin allowed Nish to get above Mulgrew to head back across the goal with the ball slipping just wide of the post.
Hibs went 2-1 ahead on 80 minutes totally against the run of play. A clever throughball from second half substitute Dean Shiels found Fletcher whose shot was parried by Langfield into the path of Riordan.
His effort was flicked goalwards by van Zanten where Mulgrew was adjudged to have handled on the goal-line. The full-back was rightly sent off before Riordan scored his second goal of the afternoon.