The Dons conceded an early goal to Ryan O'Leary before going on to dominate the game with three second-half goals securing a well-deserved win.
Two goals inside 11 minutes at the start of the second half from Gavin Rae and Niall McGinn put them ahead before a last-minute strike from Scott Vernon wrapped up the points for Craig Brown's side and stretched their unbeaten run to eight games.
With only one defeat between them from their last five league games, an entertaining game was anticipated from these in-form teams.
And the fans were not disappointed in a blistering start and an entertaining finish.
Within 60 seconds McGinn, with two goals in his last two games, might have opened the Dons' account. But after nipping in behind Michael Nelson he lashed the ball high over Kyle Letheren's goal.
In the third minute the home side found the target with a rather fortunate goal. Gary Harkins hit a stinging drive from the edge of the box which Jamie Langfield dived to punch out but the ball rebounded off O'Leary and carried over Langfield and under the bar to put Killie ahead.
Aberdeen, though, looked comfortable in possession and carved out the best of the chances for the remainder of the half.
An inswinging cross from Ryan Fraser was glanced on by Scott Vernon but Letheren saved low at his post.
The home keeper looked less than comfortable after 18 minutes when 18-year-old Fraser whipped in a free kick which Letheren fumbled before Liam Kelly booted the ball clear.
For the latter part of the half McGinn found plenty of space on the right hand side but a series of tempting crosses from the former Celtic midfielder found no takers.
Then just before half-time, and with the home side down to 10 men as Cillian Sheridan received treatment for a head cut, Aberdeen passed up their best chance of the first period. This time McGinn's pass found the inrushing Rae but he swept his shot wide when he should have equalised.
Within a minute of the restart Rae had atoned for that missed chance when Aberdeen deservedly grabbed the equaliser. Nelson lost control inside his own box and when the ball rolled to Rae he gratefully accepted the chance, slamming the ball past the exposed keeper to make it 1-1.
That sparked some much-needed life into the home side and a curling free-kick from Harkins forced a fine diving save from Langfield.
It was the Dons, though, who grabbed the lead after 56 minutes. A lovely floated ball from Fraser found McGinn ghosting in behind O'Leary and from six yards he guided his header past Letheren to make it 2-1.
McGinn almost made it three on the hour but his powerful angled drive was brilliantly palmed over the bar by the Killie keeper.
As the home side pressed for the equaliser the Dons defence, expertly marshalled by Russell Anderson, stood firm.
In the final minute the Dons made sure of the points when Scott Vernon worked a one-two with Johnny Hayes at the edge of the box before calmly curling the ball low into the keeper's left hand corner to make it 3-1.
