Andrew Barrowman opened the scoring with five minutes remaining in the first half and Joe Cardle doubled the visitors' lead on the hour mark.
With three minutes remaining Liam Buchanan added a third to ensure Dunfermline's first ever Scottish Premier League victory at Rugby Park.
After a drab opening to the match, Dunfermline had a good opportunity to break the deadlock when David Graham seized on deflected through ball but was denied a shot on goal by a wonderful tackle from Zdenek Kroca.
Dunfermline breached the home defence again minutes later but Buchanan's control let him down after rounding Cammy Bell in the Kilmarnock goal.
It took the hosts 12 minutes to produce their first attempt on goal, Ben Gordon firing over from outside the box.
Dunfermline responded at the other end but Cardle's effort was well over the top.
The visitors had a glorious opportunity to open the scoring after 39 minutes when Cardle's free-kick broke to Barrowman but his close-range effort was saved brilliantly by Bell.
The striker made no mistake when presented with another good chance two minutes later.
The Kilmarnock defence was caught out by Paddy Boyle's long ball and Buchanan's cut-back was finished in style by Barrowman.
Kilmarnock almost hit back immediately through Paul Heffernan but his low drive was brilliantly kept out by Iain Turner.
Garry Hay then tried his luck from distance but Turner again produced a good stop to deny the home side an equaliser.
After a disappointing start to the second half, Kenny Shiels made a double switch, introducing James Dayton and David Silva for Hay and Liam Kelly.
Barrowman passed up a great chance to double his goal tally and Dunfermline's lead after 56 minutes.
Kroca's slip on the edge of the penalty area allowed Buchanan to slide the ball to the former Ross County striker who somehow missed the target from two yards out.
On the hour mark the visitors increased their lead after another defensive error from Kroca.
The Czech defender attempted to usher the ball out of play but Buchanan was able to intercept and he laid the ball to Cardle who slotted home.
Kilmarnock began to increase the pressure on the Dunfermline goal as the home fans' frustration became increasingly evident.
Substitute Dayton flashed a shot wide of target and then minutes later headed past the post from Ben Gordon's cross.
The visitors continued to look dangerous on the counter-attack and on 74 minutes Bell had to make a smart stop from Cardle's stinging shot.
With 10 minutes remaining Heffernan looked to be denied a clear penalty when he was felled by Boyle and referee William Collum waved play on.
Dayton then again came close when he jinked into the Dunfermline penalty area and unleashed a powerful shot which was blocked by the back of Alex Keddie.
Dunfermline confirmed the win with three minutes remaining as Cardle slipped the ball inside to Buchanan and he finished emphatically.