Colin Nish gave Killie the lead shortly after half-time, but Shunsuke Nakamura and Kenny Miller responded to clinch maximum points for the champions.
There were few clear-cut chances in a first half of fierce commitment.
Jiri Jarosik's only contribution to the opening 45 minutes was a sublime spin which turned the entire Killie defence. He then fed Stephen Pearson, who took too long to line up his shot and James Fowler slid in with a beautiful tackle.
Killie came closest in the first half when Garry Hay latched on to Graeme Smith's quick clearance and crossed for Steven Naismith, whose first touch bounced waist high. He still managed to poke the ball beyond Artur Boruc, but it bounced back of the crossbar.
The home side were rocked in the final minutes of the first half when in-form David Fernandez was stretchered off the field as a result of a reckless challenge by Gary Caldwell, for which he was lucky to only see yellow.
His replacement, Nish, wasted no time in making an impact as he scored four minutes after the restart.
He stole the ball from Nakamura and fed Peter Leven. The midfielder ran past Neil Lennon before laying the ball back into Nish's path and the striker stroked the ball below the keeper's grasp.
Nakamura made amends for his error ten minutes later when he curled a perfect free-kick inside Smith's right post for the equaliser.
Kilmarnock tired in the final quarter and it was no surprise when Bhoys substitute Miller slid in to convert Shaun Maloney's low cross in the 75th minute and win the game.