Aberdeen manager Jimmy Calderwood rested several of his first-team regulars following their midweek European defeat and may be ruing that decision after a disjointed display.
The game started in spectacular fashion with four great chances inside the first ten minutes.
Killie could have scored twice in the first three minutes. First Allan Johnston was denied after a great through ball from Craig Bryson, before Garry Hay's delicious cross from the left found Danny Invincibile inside the six-yard box, but the Aussie striker could get enough purchase on his header.
A minute later, it was the Dons' turn to threaten and Darren Mackie's acute-angled shot beat Alan Combe, but Jamie Hamill got back to deflect the ball wide.
Aberdeen were completely disorganised defensively and it was no surprise when Killie took the lead in the 14th minute with a cheap goal.
Hamill's strong tackle won the ball for Mehdi Taouil and he sent the young full-back clear on the right.
He duly whipped in a good ball to the far post where Bryson was unmarked and he volleyed low past Derek Soutar.
Calderwood was forced into a drastic change of tactics and he substituted a disconsolate Josh Walker as he reverted to a flat back four.
This reduced the regularity of the Killie attacks, but the home side were full of confidence and doubled their lead before half-time.
Soutar made a great block to deny a Hamill volley, but the Dons defence was slow to react and Bryson crossed for Fraser Wright to head home from close range.
Aberdeen should have got themselves back into the game ten minutes after the break when Barry Nicholson's corner found Lee Mair six yards out, but his header flew over.
Killie went straight up field and Taouil and Johnston combined again to put Johnston through on the keeper, but Soutar made a good smothering block.
Kilmarnock wrapped up their most comfortable win of the season in the 75th minute with Bryson's second.
Invincibile broke clear on the right and sent over a perfectly weighted pass for the midfielder to stab home at the far post.
Aberdeen scored a bizarre consolation goal when Combe failed to collect a harmless Jeffrey de Visscher cross and watched it roll into the back of the net.