The game was spoiled as a spectacle due to a difficult swirling wind allayed by driving rain making silky soccer almost impossible.
Dons boss Jimmy Calderwood will be delighted by the desire and effort his side put in during the second half after going in 1-0 down at the interval.
In the visitors' camp, manager Jim Jefferies will be aggrieved that his side had looked comfortable for the first hour before conceding a poor penalty kick after failing to clear the ball from their own area.
After a fairly non-descript opening with the home side holding the upper hand without testing Alan Combe in the Killie goal, it was the visitors who had loud claims for a penalty kick after 15 minutes.
Colin Nish and Lee Mair tangled on the edge of the Dons box with the big striker appearing to have been impeded as he advanced on goal.
The Killie dugout was furious on the halfway line with both manager and assistant having to be restrained by the fourth official.
Aberdeen didn't heed the warning when an excellently driven cross from James Fowler found the head of David Fernandez who bulleted a header home from six yards.
The brought the home side to life as they forced the visitors on to the back foot.
From a Barry Nicholson corner, Lee Miller rose above his marker only to fail to hit the target from six yards.
Good possession through midfield almost brought an opening after 38 minutes when Michael Hart and Derek Young combined to play in Chris Maguire, but the striker snatched at his 14-yard effort which flew harmlessly wide.
As the game approached half-time, the Dons almost got an unlikely lifeline when a Young cross was headed just over his own crossbar by Fraser Wright.
Aberdeen boss Jimmy Calderwood made a couple of changes at the interval when he brought on the experience of Steve Lovell and Scott Severin at the expense of youngsters Sone Aluko and Maguire.
The changes almost paid dividends after 52 minutes when Miller headed the ball into the path of Lovell, but under pressure from a Ryan O'Leary the substitute hooked his shot well off target.
Killie paid the price for defending far too deeply in the second half when the home side drew level on 63 minutes.
Miller was upended inside the box by Jamie Hamill giving the referee Willie Collum no option but to award a penalty kick.
Barry Nicholson strode forward to confidently drive home the resultant spot-kick.
Aberdeen were turning the screw now and came close again on 72 minutes.
Chris Clark got to the byline before clipping in a dangerous cross which found the head of Richie Byrne, but his flashing header flew just wide of the uprights.
With the visiting defence struggling to cope with wave upon wave of home attacks, the Dons got their noses in front in 75 minutes.
Young played the ball in from the right onto the head of Miller whose downward header gave Combe no chance.
In stoppage time, Killie almost snatched an unlikely equaliser when Nish sent Ryan Jarvis racing into the box, however from a tight angle, he couldn't keep his shot on target.