The Killie youngster calmly slotted home from the spot after being brought down by Craig Gordon to deflate the Jambos, who had enjoyed the bulk of the play.
Killie were unusually sloppy in defence in the first half with Gordon Greer and Ryan O'Leary having to make desperate last-ditch tackles to deny Roman Bednar after gifting Hearts the openings.
Neither side created any clear-cut chances in the first period, but Saulius Mikoliunas will feel he should have done better than scuff the best opportunity weakly into Alan Combe's arms.
Hearts produced their best move of the match in the 52nd minute but it ended in Bednar again being denied by a desperate tackle, this time by substitute Garry Hay when a goal looked likely.
It looked even likelier five minutes later when Combe missed a free-kick and the ball fell to Andy Driver, but he couldn't get the ball out of his feet and the defence recovered.
Killie carved out their first chance in the 72nd minute when Fraser Wright rose to meet Gary Locke's corner, but Gordon was perfectly placed to save.
Momo Sylla escaped a red card a minute later when he cynically brought down Driver, but referee Collum ducked the decision.
He had no choice but to make a decision to give Kilmarnock a penalty in the 82nd minute when Naismith took advantage of hesitant defending to be brought down by the keeper.
The young star tucked the ball home from the spot, beating Gordon's despairing dive giving Killie a fine end to the season with three consecutive victories.