The first half began quietly but home keeper Alan Combe produced an international class save in the 13th minute to deny ex-Killie favourite Craig Dargo, as he somehow touched the little striker's flicked volley round the post.
Inverness snuffed out Killie's five-man midfield in the first half and were deservedly ahead at the break.
Jim Jefferies was still giving the instruction on the half-hour to switch to a back four when Dargo turned neatly inside his marker and unselfishly passed square to Graham Bayne, who finished neatly low past Combe.
Killie lacked their normal fluency and it took until the final minute of the half for them to force Caley keeper Mark Brown into action, when he had to race smartly off his line to thwart Steven Naismith after Allan Johnston's clever pass.
Coin Nish replaced Rhian Dodds in an attacking half-time change, and Killie carried far more threat in the second half.
The Caley defence coped comfortably with any crosses Killie could deliver up until the 54th minute and they will be furious with the way they conceded the equaliser.
Johnston's cross from deep deceived the defenders and goalkeeper alike, allowing Kris Boyd to ram home his fifth goal in three games from one yard out.
And as Killie have done so often season, they followed up one goal with another two minutes later. Again Johnston was the architect, lifting the ball over the bewildered back line for Naismith to score with an angled shot.
Caley looked to have lost their urgency, but bounced back in the 77th minute. Barry Wilson crossed from the left and Dargo dived from the edge of the six-yard box to head into the corner of the net.