Killie goalkeeper Alan Combe took a heavy knock in the early stages which saw him replaced at half-time.
The short-term consequence of the challenge was felt in the 14th minute when Combe stayed on his line instead of collecting a regulation cross from Don Cowie, and the ball reached Dougie Imrie beyond the far post.
He had full-back Garry Hay between him and the goal, but he struck his shot well and the ball cannoned off the sliding defender and the crossbar before bouncing into the roof of the net.
Caley's midfield trio of Ian Black, Imrie, and Iain Vigurs were winning every loose ball and, as a result, it was the Highlanders who were rampant, although they could not craft any real chances.
They got the second goal they deserved in the 38th minute, and again it was Combe's hesitancy under the high ball that cost Killie.
Cowie launched a rugby-style Garry Owen into the goalmouth, and Combe went up to catch under pressure from striker Garry Wood. The keeper dropped the ball, and it bounced off the striker and over the line.
Killie's only real shot at goal in the first half came in the 40th minute when David Fernandez wriggled away from Ross Tokeley. He had options to his left, but opted to shoot on his weaker right foot, and Ryan Esson held his shot comfortably.
The hard work done, Inverness were content to sit back and soak up what little pressure Kilmarnock could muster.
Wood almost scored his second in the 63rd minute on a rare break forward. Imrie crossed from the right and found the striker, but replacement keeper Damien Rascle made a brilliant block on the line.
Caley keeper Esson had to make a great save of his own four minutes later to block Manuel Pascali's powerful header, and had to react sharply again to tip Fraser Wright's effort over the bar from the resultant corner.
Killie's afternoon was summed up in the 72nd minute when Fernandez found James Fowler free in the box, but the midfielder embarrassingly missed the ball completely.
Substitute Willie Gibson clawed a lifeline for the home side with five minutes left when he finished off a nice passing move with a powerful low drive from the edge of the box which nestled in the bottom right corner of the net.
Gibson was then brought down in the box in the 89th minute by a trailing leg. Mehdi Taouil stepped up to earn his side a point from the penalty spot, but blazed his kick over.