Credit must go to the visitors who bounced back from their defeat last week to pick up all three points in a smash and grab victory. Killie stuck to their game plan and picked off Aberdeen on the counter attack to register an unlikely win.
Aberdeen were able to call upon the services of fit-again Steve Lovell up front, the ex-Dundee man making his competitive debut.
Disaster struck for the home side within 30 seconds of kick-off. Russell Anderson played the ball back to Alexander Diamond who, without looking, hit his pass back too short. Diminutive striker Allan Johnston latched on to the ball before sliding it under the advancing Ryan Esson for the opener.
Aberdeen's response was immediate, but Anderson was way off target with the header from Jamie Winter's cross.
Only a superb stop by Alan Combe in the visitors goal after 14 minutes stopped Aberdeen drawing level.
A short free kick from Barry Nicholson into the path of Chris Clark saw the midfielder fire in a brilliant effort from 30 yards which the goal keeper did well to parry.
As Aberdeen upped the pressure, Combe again did well after27 minutes, coming to collect a dangerous Nicholson cross just ahead of Steve Lovell. In the next minute, Jamie Smith wasn't far off target with a rasping 22-yard effort which flashed just past the upright.
Aberdeen finally hauled themselves level after 34 minutes. A Gary Dempsie corner was not cleared by the Kilmarnock defence, and Dons skipper Anderson latched on to the loose ball to drive home from six yards.
Aberdeen should have gone ahead after 50 minutes, but Nicholson's point blank header from McNaughton's cross flew straight into the arms of Combe. In the following minute Combe again saved his side when he somehow kept out a flashing header from Lovell at his near post.
Aberdeen almost gifted the visitors the lead after 66 minutes when Kris Boyd dispossessed Scott Severin. The big striker drove into the Dons box before toe poking an effort on the wrong side of the upright.
Kilmarnock broke away to score the winning goal after 72 minutes. Colin Nish won the ball in a tackle against Anderson, the ball breaking to Johnston who released Steven Naismith just inside the Dons half. The youngster carried the ball 40 yards before slipping it past Esson.