Jim Jefferies had his young guns to thank as Craig Bryson and Iain Flannigan inspired their come-from-behind victory.
Kilmarnock's Mehdi Taouil had the first chances of the match, in the seventh minute following a quick one-two with Flannigan where his shot slid wide.
Then with a lob from the edge of the area which sailed over after Caley keeper Michael Fraser had punched weakly at a Garry Hay cross.
Thistle went ahead in controversial circumstances in the 14th minute with a hotly disputed penalty. Ross Tokely and Frazer Wright collided going for a loose ball in the Killie box and referee Tom Murphy somehow adjudged that the big Highlander had been fouled and pointed to the spot.
Ian Black made a perfect job of the spot-kick, sending Alan Combe the wrong way.
Inverness had a stronger appeal for another penalty turned away soon after, when Black appeared to be hauled down by Tim Clancy.
Killie fought back and drew level in the 38th minute when Wright was alert to pounce on the rebound when Flannigan's excellent 20-yard free-kick cannoned off the post to knock the ball home.
The referee was in the spotlight again three minutes after the interval when Flannigan was denied a goal by Roy McBain's blatant handball on the goal-line, but Mr Murphy appeared to be the only man in the stadium not to see it.
Killie midfielder Bryson got him off the hook two minutes later by giving his side the second goal they felt they had been denied. He struck a glorious 30-yard shot which bounced in front of the diving Fraser and nestled in the corner of the net.
Bryson was instrumental in rampant Killie's third goal in the 56th minute. Clancy made good ground on the right and cut the ball back to the edge of the area, where Bryson guided the ball towards goal.
Fraser looked have the shot covered until it struck Phil McGuire and spun past the keeper.
Killie were full of confidence now and Flannigan blasted home number four after a flowing move involving Taouil and David Fernandez.