However, the Dons' Jamie Langfield was by the far the busier keeper in the first half, making two excellent saves.
He made his first notable save in the 26th minute after he had dropped a cross, but reacted well to block David Lilley's effort.
His most telling impact came in first-half stoppage time when Russell Anderson missed a high ball, and it fell kindly for Steven Naismith who shot powerfully, but Langfield made a great diving block.
The second half began in the same vein with Killie in charge, and it was a major surprise when they fell behind in the 59th minute in the cruelest of circumstances.
James Fowler's attempt at a cute header back to Graeme Smith went horribly wrong, and the ball evaded the keeper and rolled gently over the line.
The match exploded in the 70th minute after another Aberdeen break. The already booked Richie Byrne was involved in an off-the-ball tangle with Momo Sylla.
The referee only saw the last act of the spat when Sylla tripped the Dons defender and booked the Killie man. To add insult to Killie's perceived persecution, the Dons doubled their lead from the free-kick.
Darren Mackie retrieved Scott Severin's delivery and fired back into the danger area where Anderson stabbed the ball home.
The controversy was not over yet, as Killie were awarded a penalty five minutes from time, thanks to the lineman's intervention.
The referee had turned away when a Killie corner was cleared, but was called back by the assistant and the penalty was given. Naismith calmly sent the keeper the wrong way.