Killie boss Jim Jefferies rang the changes in the home side after losing in the Cup to Motherwell at the weekend, bringing in Garry Hay, Gary McDonald and Barry McLaughlin.
In addition, Colin Meldrum replaced the injured Gordon Marshall, and Jefferies changed the shape of his side to an attacking 3-5-2 formation.
It took a penalty goal to separate the two sides in a drab game at the weekend, and so it proved again.
Killie looked uncomfortable in the opening 20 minutes, but as they adjusted to the new formula, they penned the visitors into their defensive third although it was not until the 35th minute that Well keeper Francois Dubourdeau was called into action, when he got down smartly to deny Hay following the full-back's well struck effort from the corner of the penalty box.
Motherwell were restricted to long-range free-kicks from Derek Adams in the first half which Meldrum dealt with confidently.
Motherwell came close in the 57th minute when Keith Lasley struck a fine half-volley which flew narrowly wide.
Craig Dargo had a chance for Killie a minute later after indecision in the Well defence, but a poor first touch pushed the ball into the keeper's hands.
The match erupted in the 79th minute when Dubourdeau elbowed Dargo in the face after the little striker had challenged for a cross ball.
Referee John Rowbotham had no hesitation in showing the keeper the red card and awarding a penalty. Kris Boyd kept his cool to send substitute Stevie Woods the wrong way from the spot.