Kilmarnock's pressure on the Dunfermline goal eventually paid off just three minutes from time when veteran goal-scorer Ally McCoist grabbed the opening goal from just six yards out.
Kilmarnock goalkeeper Gordon Marshall returned from suspension but found he had been relegated to the bench in favour of Colin Meldrum.
Former Airdrie midfielder Antonio Calderon was handed a place in the starting line-up on his debut.
The Pars enjoyed the first attack of the game after four minutes when Gary Mason went on a good run down the left wing before squaring the ball to Tomas Danilevicius in front of goal but the danger was cleared by Frederic Dindeleux.
Killie tried to push forward and Andy McLaren was looking dangerous but they struggled to create much in the way of clear-cut chances in the opening period.
Mark Reilly had the chance to threaten the Dunfermline goal with a free kick after 15 minutes but sent the ball past the post.
Dunfermline stand-in skipper Scott Thomson looked to have taken a painful blow after 20 minutes when he was caught by his own goalkeeper Marco Ruitenbeek who was trying to clear a corner.
But the Pars player was quickly able to return to action.
A few minutes later Dindeleux went on a great surging run but his final shot was weak and easily held by the Dunfermline goalkeeper.
Ruitenbeek was forced to come to the rescue again two minutes later to block McLaren's header from inside the six-yard box.
Kilmarnock were looking more threatening now and Garry Hay could have put them ahead with a well-taken effort but he pulled the shot just wide.
Thomson was obviously still feeling the effects of his earlier clash with the goalkeeper and he had to be replaced by David Moss after 34 minutes.
But Kilmarnock were still piling on the pressure and a minute later McLaren saw a decent shot deflected off defender Andrius Skerla.
But the breakthrough eventually came after 42 minutes when Alan Mahood's cross found McCoist just six yards out and the veteran goal-scorer fired past the goalkeeper.