David Proctor came into the midfield in place of the injured Richie Hart and Canadian Richard Hastings took over from the suspended Grant Munro. Killie had to do without striker Kris Boyd who failed a late fitness test.
In a dull opening Craig Dargo for Killie and Richard Hastings for Caley came closest.
Craig Brewster then forced Alan Combe into a save on 14 minutes with a 16-yard shot.
Bryan Prunty headed into the net on 18 minutes when Ian Black crossed but he was offside at the time.
Moments later Killie snatched an unlikely advantage. Gary Wales back heeled to James Fowler and he passed into Gary McDonald who gave the visitors the lead.
However, Caley pulled it level on 28 minutes when Ross Tokely converted a spot kick after Darren Dods' jersey was held in the box and the teams went in at 1-1 at the break.
In a dull second half, substitute Graham Bayne missed the target with a header where chances were few and far between.
On 72 minutes Peter Leven scored from the spot when McDonald's jersey was held in the box.
Caley Thistle did try to hit back. Bayne and Prunty both hit woodwork after Brewster's drive was knocked off the line and Barry Wilson's follow up was held by Combe.
In the end, it was the Rugby Park side who held on for victory.