An inspired Ebbe Skovdahl substitution proved to be the decisive moment, turning a sub-par match into a second-half cracker.
Kilmarnock had controlled the whole of the first half and Peter Canero had gone close as early as the 2nd minute, firing a great 25-yard drive which saw David Preece fly to his left and parry to safety.
Despite the dominance they had only an unsuccessful penalty claim to show for their efforts before the break, when a Gary McSwegan shot was deflected behind by Phil McGuire's outstretched arm. But the referee ruled that it was unintentional.
The second-half started in the same manner as the first had finished, but this time Killie made their advantage count. McSwegan's low cross found Kris Boyd, who was pulled off the ball by McGuire. As the home fans yelled for a penalty Alan Mahood kept playing and smashed the loose ball past the stranded keeper.
Skovdahl then played his masterstroke replacing his strikers with Ben Thornley and Scott Michie. And within sixty seconds his side had equalised. A simple ball over the top caught out the Killie central defence and Laurent D'Jaffo burst through to stab the ball past Gordon Marshall.
The goal gave Aberdeen heart and they began to push forward. Eric Deloumeaux hit the outside of the post before Darren Young latched on to a weak headed clearance and sent a beautiful 35 yard shot sailing into the keepers' top left-hand corner.
The home team then threw caution to the wind and were rewarded in the final minute, when Barry McLaughlin met Jose Quitongo's cross to power home a header from inside the six yard box.
Paul Di Giacomo could then have won it for the home team in injury time, but missed his kick in front of goal