The Highland Capital side were looking to build on last weekend's draw against Celtic, but amidst short flurries of heavy snow, the game did not really come to life until just short of the half-hour mark.
Dougie Imrie wasted the game's first real chance on 27 when he was sent clear by David Proctor, but from just inside the box he unleashed a shot that flew high over the crossbar.
On a pitch now more white than green, the yellow ball had to be introduced and the change seemed to spark Caley Thistle into life.
A free-kick on the left after 35 minutes was taken by Ian Black and Pavels Mihadjuks rose highest in the six-yard box to head home his second goal in three games.
Five minutes later Russell Duncan was a whisker away from putting Inverness into a commanding position, but his low drive narrowly failed to find the corner of the net.
Having made himself a hero, Latvian Mihadjuks then looked to have turned villain after appearing to fell David Fernandez just inside the box right on the interval.
Referee Iain Brines seemed to indicate he had awarded a penalty, but following protests by the home players, changed his mind and gave a free-kick right on the edge of the area.
After all the commotion surrounding the incident had calmed down, Willie Gibson took the set-piece only to strike his effort straight at Inverness goalkeeper Ryan Esson.
Killie's problems worsened as Fernandez failed to come out for the second half, Allan Russell taking his place in the visitors attack alongside Kevin Kyle.
It still failed to bring to life an insipid Killie with Esson in the home goal having very little to do as the hour mark approached, although Alan Combe at the other end was equally quiet.
The ball seemed to be spending more time in the air than on the ground, but interest from the supporters was reignited when Kilmarnock's new signing Kyle was shown a straight red card for elbowing David Proctor in the face.
The visitors, however, responded to going down to 10-men positively with Gavin Skelton forcing Esson to parry away his 25-yard shot on 71 minutes.
Ten minutes later, Black was perfectly positioned on the goal-line to clear a Manuel Pascali header.
Despite late opportunities for Killie, Caley Thistle sub Adam Rooney made the game safe for the hosts a minute from time, thrashing home Proctor's cross.