Lee Bullen's missed spot-kick in the 50th minute cost Dunfermline dear at Rugby Park.
The Fifers, sitting in third place in the SPL will see this as two points dropped rather than one gained.
Craig Brewster's 43rd minute strike had set his side up perfectly at half time, but an incident-packed start to the second half brought the match to life.
The match began quietly, with a midfield battle of few goalscoring chances before Brewster latch on to Gary Dempsey's throughball to open the scoring two minutes before the break.
Killie manager Jim Jefferies changed his system and brought on his two wingers Jose Quitongo and Stephen Murray at half time to threaten the Dunfermline rearguard and he saw his side pull level within two minutes of the restart.
Former Pars favourite Greg Shields crossed from the right touchline, but the ball swerved wickedly and Marco Ruitenbeek was wrong-footed in the Dunfermline goal and could not prevent the ball from nestling in the corner of the net.
Dunfermline went straight upfield from kick-off and were awarded a penalty when Dempsey was upended by goalkeeper Gordon Marshall, only for the veteran to rectify his mistake by pulling off a great save low to his right from Bullen's kick.
But Bullen received reparation himself in the 57th minute when he was on hand to hammer the ball home after Marshall could only parry Dempsey's 20-yarder out in front of goal.
Jeffries introduced Kris Boyd for the struggling Gary McSwegan and was rewarded within five minutes as the young striker grabbed the equaliser in the 76th minute.
Gary Locke's corner was headed on by home debutant Samuel Boutal and Quitongo was alert to send the ball past Ruitenbeek to Boyd, who was able to scramble the ball over the line