Livewire Liam Buchanan was the inspiration as Dunfermline claimed a victory that moves them closer to Hibernian at the bottom of the table.
He pounced on a mistake by Mo Sissoko before setting up Andrew Barrowman to slot home after 42 minutes.
Good saves from Iain Turner and a goalline clearance kept the Pars ahead.
And, when Buchanan dispossessed Zdenek Kroca, he set up Joe Cardle to fire in after 60 minutes before the forward scored after an 87th-minute break.
The win ended a run of 10 games without a victory for the side who slipped four points adrift of Hibernian after losing to their relegation rivals last weekend.
Dunfermline manager Jim McIntyre responded to the midweek Scottish Cup loss to Inverness by signing Mark Kerr and the former Aberdeen, Falkirk and Dundee United midfielder was immediately handed his debut against the club with whom he had been on trial.
Buchanan and midfielder Gary Mason also came into the side - with Andy Kirk, Ryan Thomson and John Potter dropping to the bench - and the former combined with the new signing to create a couple of early openings.
Kroca's fine interception halted the first, while striker Buchanan squandered the other with some poor control after rounding goalkeeper Cammy Bell.
Ben Gordon, beginning his second loan spell from Chelsea, was straight into a Kilmarnock starting line-up also boosted by the return of Dean Shiels, Garry Hay and Gary Harkins and quickly made an impression.
The full-back looked to catch out Turner, back into the side in place of error-plagued Chris Smith, but his clever chip drifted over the crossbar.
Dunfermline, though, continued to be the more dangerous and Cardle's drive just failed to dip sufficiently to worry the bar.
Buchanan was getting closer to breaking the deadlock and had a drive blocked by Bell before playing his part in the goal when it eventually came.
After a mistake by Sissoko, he rolled the ball into the path of Barrowman to score his sixth of the season.
That stung the hosts and they had Dunfermline under siege for the final three minutes of the first half.
Turner saved well from a Dean Shiels drive, Mason cleared off the line from a Liam Kelly effort then the goalkeeper saved well to deny Hay.
However, Dunfermline ought to have extended their lead early in the second half when Buchanan made room for himself and set up Barrowman at the front post, but the former Kilmarnock striker shot wide.
Buchanan was proving a constant irritant to the Killie defence and set up the Pars' second goal, although they were again given a helping hand by the home side.
The former Partick Thistle forward robbed Kroca as the big defender tried to let the ball run out for a corner before setting up Cardle to settle himself before firing past Bell.
A James Dayton header flashed wide of the Dunfermline goal after he met a fine Gordon cross.
Dunfermline went close to extending their lead when a superb save from Bell thwarted Cardle's sweetly struck effort from long range.
Kilmarnock had a shout for a penalty turned down after Paul Heffernan went down in the penalty box in the closing minutes before Buchanan rounded off the victory.