Rory Fallon gave the Dons and early lead, but Paul Heffernan netted five minutes before the break to punish the visitors for their profligacy.
The visitors made a strong start and Fallon should have done better after getting on the end of a pinpoint delivery from Stephen Hughes, before Cammy Bell made a brilliant save to deny Rob Milsom.
But just seven minutes in Fallon spotted Bell off his line and beat the Killie keeper with a superb volley from distance.
Niall McGinn then cruised into the box and unleashed a shot that beat Bell before striking the post, before Jamie Langfield made his first save when he turned Heffernan's shot round the post.
The Dons spurned another golden opportunity when Joe Shaughnessy prodded past the post from Ryan Jack's cross.
Killie levelled when Mohamadou Sissoko's pass found William Gros and his heavy touch made its way to Heffernan to flash the ball past Langfield.
Kilmarnock had yet another close escape as Sissoko made a fantastic clearance from McGinn's goalbound strike and Bell produced a late point-blank save to thwart Johnny Hayes.
In between those efforts Aberdeen had a strong penalty claim turned down when Bell appeared to catch McGinn, who was instead booked for simulation by referee Euan Norris.