The Dons opened the scoring when Scott Vernon's shot squeezed past Cameron Bell after 15 minutes before Sone Aluko added a second with a low drive 10 minutes later.
Chris Maguire netted a third from the spot after 59 minutes after he had been brought down in the box by Frazer Wright before Rory McArdle scored the fourth from close range with 19 minutes remaining.
Substitute Josh Magennis added a fifth in the closing stages as the Dons recorded only their fourth win at home in the SPL from 12 matches.
The Dons were without Paul Hartley following his red card in the 2-1 defeat to Motherwell on Tuesday.
Rob Milsom was his replacement, while Derek Young and Rory McArdle were also handed starts in place of striker Nick Blackman who dropped to the bench and defender Nikola Vujadinovic who missed out altogether.
Killie's creative midfielder Alexei Eremenko, who had been suspended, and defender Wright, who had two weeks off after suffering concussion, returned, with Jamie Hamill and Manuel Pascali starting as substitutes.
Prior to the match, Aberdeen boss Craig Brown had said Kilmarnock's attractive style made them the closest thing the Scottish Premier League had to Barcelona. However on a wet and wild day in the Granite City, it was evident early that the Pittodrie pitch would not be conducive to passing football.
The Dons survived an early scare when Kieran Agard raced on to a searching pass from Eremenko and knocked the ball past the advancing Jamie Langfield but, just as the striker on-loan from Everton looked set to roll the ball into the unguarded net, he was tripped by Zander Diamond.
Surprisingly the defender escaped without even a caution, with Langfield making a terrific save to keep out Eremenko's effort from the free-kick.
The Dons went ahead when Wright failed to deal with Ryan Jack's low cross into the box and Vernon's drive on the turn squirmed past Bell.
Maguire should have doubled his side's advantage five minutes later when he was released by Aluko but the striker dragged his volley wide.
However Aluko did net a second when Kilmarnock were caught out trying to pass their way out of a defence and the Dons winger pounced on a loose ball before fizzing a low shot past Bell.
Aberdeen were bossing proceedings against a shell-shocked Killie with Maguire, eager to add his name to the scoresheet, volleying wide before Mohamadou Sissoko did well to intercept Jack's inviting ball into the penalty area with Vernon lurking.
There was still time before the break for McArdle to pick up the first booking of the match for a push on Agard.
The visitors made two changes during the break with Pascali and Hamill introduced at the expense of Rui Miguel and Liam Kelly.
The substitutions and a bold switch to a more attacking formation gave Killie fresh impetus and they dominated the early exchanges of the second period without managing to work Langfield.
But the Dons added a third after 59 minutes when Maguire was brought down in the box by Wright, who appeared fortunate to only be shown a yellow card for making the foul, and the striker sent Bell the wrong way from the spot.
Things got even better for Aberdeen after 71 minutes when Aluko's cross to the back post was nodded across goal by Vernon for McArdle to turn the ball home from close range.
There was still time for Aberdeen to add a fifth after some more woeful defending by Kilmarnock when substitute Josh Magennis pounced on an error by Garry Hay to drill the ball past Bell.
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