Kilmarnock's top scorer Kris Boyd's knee injury caused him to miss his first match in over a year.
Danny Invincibile took his place up front while Stevie Murray slotted in on the wing and Shaun Dillon made a rare start in place of the Garry Hay.
Dunfermline's reaction to their UEFA Cup disappointment was to drop Scott Wilson and Derek Young in favour of Richie Byrne and Billy Mehmet.
If the Pars were keen to make up for their European embarrassment, it didn't show in the early stages as they appeared lethargic and jaded.
Invincibile was relishing his central role and gave Andrius Skerla a torrid time, and it resulted in the only goal of a scrappy encounter.
Killie keeper Allan Combe rushed from his line to clear a Dunfermline attack. His clearance stayed in play wide on the Killie left and Invincibile muscled Skerla off the ball and careered into the penalty box. He cut inside the last defender before wrong-footing Stillie.
Dunfermline lacked any guile with Craig Brewster looking an isolated figure, often standing on the ball with no options ahead of him. They were restricted to long-range shooting, with only Gary Dempsey's 25th minute strike stretching Alan Combe.
Killie full-back Dillon brought a good save from Stillie in the 32nd minute with a 25-yard thump, but Murray should have given the home side a more comfortable half-time lead when Gary MacDonald's perfectly weighted pass sent him clear in the area, but he shot wildly past the upright.
There was little quality football played in the second half as Kilmarnock retreated into their shell as the Pars pushed forward searching an equaliser.
It almost came in the 53rd minute. Gary Wales was booked after a deliberate hand-ball at the edge of his own area. Brewster hammered a fierce shot past the wall which seemed to send Combe the wrong way, but the keeper somehow managed to change direction and punch the ball to safety.
Dunfermline continued to press and the Kilmarnock defence was in tatters, but still the equaliser wouldn't come.
Kilmarnock had the clearer opportunities late on as they hit on the break. Invincibile was at the heart of all Killie's best attacks. Stillie did well to touch his shot behind in the 70th minute, but he should have done better than head wide from the subsequent corner.
Allan Johnston picked the Australian out at the far post with a measured cross and substitute Craig Dargo was inches away from scrambling the knockdown over the line.
Andy Tod had the chance to score the goal his team deserved in the 85th minute, but he dallied for too long on the ball and James Fowler and Combe combined to block his shot.
Combe nearly undid all his previous good work as he dropped the ball in the dying minutes, but with Dunfermine's luck as it is just now, it rolled past the post.