The home side took an early lead through a John Sutton strike, and a Ross Forbes penalty gave Well a crucial two goal half time advantage.
Killie improved after the break thans to a tactical change, but were hit by a sucker punch as the nmatch entered the final quarter as Shaun Hutchinson fired home after Kilmarnock failed to clear a corner, leaving Jamie Hamill's delicate chip two minutes from time scant consolation for the large travelling support.
Poor defending was at the root of Killie's problems, with Steven Old inparticualr having a first half he will want to forget. The right back was faced up to by the pacey Jim O'Brien, and the New Zealander was found wanting. O'Brien nipped away from his marker far too easily from a fifteenth minute throw in to feed Sutton who finished well.
Killie dug in and kept a rampant home side in check, but a chronic lack of width meant that any attack were easily mopped up by a resolute defence.
It looked as though Killie would go in only one down at half-time until O'Brien got behind Old in stoppage time. The winger was heading away from goal, but Old made a clumsy challenge and brought his man down for an easy penalty award. Cammy Bell guessed right, but couldn't stop Ross Forbes's kick.
Old was unsurprisingly replaced at half-time by Danny OInvicibile with Hamill reverting to full back, and the move paid dividends with Killie utilising the flanks for the first time. Invincibile almost brought Killie back into the game within five minutes of the restart with a snap shot which just rolled the wrong side of the post.
Killie striker Kevin Kyle then had two chances, but he failed to get over a header which landed on the roof of the net, and then hit a scuffed left foot shot on an rare off day in front of goal.
Conor Sammon was Killie's most effective player, but he too fluffed his lines in front of goal as he scuffed his shot from a good position.
Killie's slack defending came back to haunt them as Well found a killer third goal in the 68th minute. A corner from the left was whipped in and came off a Kilmarnock head and found Hutchinson at the far post who drilled the ball home.
Jamie Hamill showed the strikers how to do it when he calmly chipped the ball over keeper John Ruddy in the 88th minte, but it was too little too late.