Aberdeen made one change to the side who lost to Rangers three days ago with 17-year old Chris Maguire coming in for his first start for the Dons, replacing the injured Jamie Smith.
Kilmarnock boss Jim Jefferies shuffled his pack making three changes to the team that lost out to Motherwell on Saturday at Rugby Park.
Aberdeen teenager Maguire made a dream start in his first start when after six minutes he picked the ball up at the edge of the area, went past two defenders before curling a right-foot shot into the top corner from the edge of the 'D'.
Things got even better for the home side just three minutes later when a ball played long from the back was laid off into the path of Barry Nicholson, who took the ball in his stride before firing home low into the corner from 12 yards.
Two minutes later Nicholson almost got his second of the game with a stunning shot from the outside of his right foot when only inches wide of the upright.
On the stroke of half-time young Maguire was unlucky not to get his second of the game after being sent in on goal by Darren Mackie, Maguire sent his low shot just wide of the far post.
The second half continued as the first had ended with Aberdeen pressing forward at every available opportunity.
In 61 minutes a corner was swung in from the left-hand side which saw Lee Miller totally unmarked at the far post but his header deflected off the top of the bar and over.
Aberdeen had to wait until the 87th minute until the third goal which their play thoroughly deserved arrived.
It came after Mackie had sent the ball in to the feet of Lee Miller inside the area, he dragged the ball back and fired goalward but his shot was beaten away by Graeme Smith, Steve Lovell was on hand to put the ball away from six yards.
Aberdeen's day, however, was tarnished by the loss of a late goal which was Kilmarnock's only effort on target in the 90 minutes.
It came when the ball was headed into the box by Danny Invincible, it caught out the Dons rearguard and fell to Steven Naismith, who prodded the ball home from the corner of the six-yard box.