Dunfermline lost an early goal to their so-called bogey team and looked out of sorts ahead of next week's Scottish Cup semi-final but a flash of genius from international striker Steve Crawford still ensured that they avenged one of only two home defeats this season.
With 20 minutes remaining Crawford pounced on a lapse in concentration by Kilmarnock defender Gordon Greer and raced 20 yards before curling the ball beyond keeper Colin Meldrum and just inside the far post.
Crawford's fourth goal against Killie this season and his 16th in all, kept the Fifers in fourth place and killed off Kilmarnock's hopes of a top six finish.
Dunfermline started brightly enough with Greg Shields crossing for defender Andy Tod, whose header flashed inches over but Killie then stunned them with the sort of goal that managers hate to lose.
Eric Skora's low free kick from the left was a dangerous one although home boss Jimmy Calderwood will be furious that nobody attacked the ball, allowing Australian Danny Invincible to stay cool in a goalmouth scramble and score with his left foot.
Terrific play from Crawford almost led to an instant equaliser from Derek Young but the visitors continued to control the game and keeper Derek Stillie had to make an acrobatic fingertip stop from another Skora free kick.
If that was a turning point, another arrived five minutes before half time when Craig Brewster and Young set up Barry Nicholson whose perfectly timed run and simple finish made it 1-1.
Young wasted two more excellent opportunities as the Pars pushed hard at the start of the second period and after Invincible and top scorer Kris Boyd led a brilliant Kilmarnock counter-attack, only two desperate blocks denied Crawford and Brewster with the visitors defence fully stretched.
Crawford finally escaped with 20 minutes left although Dunfermline could never relax against a determined Kilmarnock side.
Ex-Par Colin Nish had the ball in the net barely four minutes after coming on as a substitute but he had clearly handled and was deservedly booked.