The home side faced a tough task against a Killie which had seen the visitors consolidate their position in top six.
The visitors forced an early corner which saw Colin Nish get ahead of Russell Anderson to nod just over on five minutes.
The Dons skipper gathered up a loose ball before advancing 20 yards where he then picked out Barry Nicholson wide on the right, but his dangerous ball into the area was well intercepted by Fraser Wright.
At the other end Danny Invincible waltzed past Richie Byrne on seven minutes to pick out Nish, whose presence in the area was troubling the Dons rear guard.
Aberdeen took the lead on 10 minutes with a fabulous goal. Darren Mackie and Kevin McNaughton linked up well on the right where the latter's cross into the area was cushioned down by Stevie Crawford into the path of Barry Nicholson whose fierce left-foot shot from 19 yards flew just inside the upright.
Nish passed up an excellent opportunity to get his side on level terms after 18 minutes. Invincible put the big striker clear, but with time and space he dragged his effort well wide of the target.
Home fans' favourite Byrne almost doubled the home side's advantage on 26 minutes when he lost his marker to power in a header from a Jamie Smith corner only to see his effort fly just wide of the upright.
Aberdeen conceded a soft penalty on 30 minutes which was easily converted by Stephen Naismith after Dons had needlessly upended Gary Wales.
A tremendous cross-ball from Danny Griffin found Smith, who tailed away from his marker before putting in an effort which was brilliantly taken by Alan Combe in the visitors' goal at the second attempt.
Clever play at the other end from Wales saw him drift inside before flashing in a good shot which was comfortably held by James Langfield.
Aberdeen were dealt a major blow on 48 minutes when McNaughton had to leave the field on a stretcher after receiving a head knock under the challenge of Invincible.
After a period of indifferent play Aberdeen finally made a breakthrough on 74 minutes. Smith's deep corner wasn't cleared properly by the visitors' defence allowing Anderson to bravely smash the ball home six yards out.
Aberdeen were now in full flow and only a desperate header off the line by James Fowler stopped Scott Severin adding a third for the home side.
Kilmarnock were not to be outdone, however, and they drove forward with every opportunity in search of an equaliser.
They were rewarded on 85 minutes as the Dons rear guard failed to clear a cross from Wales and it was former Don David Lilley who stooped to head past Langfield and bring the sides level again.
The visitors had a major let off in the final minute when Smith got on the end of Lilley's short header back to his goalkeeper, but Combe stood tall to secure his side a valuable point.