An own-goal by Hearts captain Danny Wilson set Killie on their way, and a double by Kris Boyd after Dale Carrick had brought Hearts level seemed to put the home side out of sight.
A goal by Sam Nicholson briefly revived the contest for Hearts, before a Michael Gardyne strike sealed the valuable three points for Kilmarnock.
There was little goalmouth action in the opening stages to warm the crowd inside a blustery Rugby Park, although Hearts should have taken the lead when some fine work down the right by Dale Carrick and Callum Paterson resulted in a corner.
Kevin McHattie's in-swinging delivery found the head of Jordan McGhee, but with time and space inside the area the right-back could only head tamely wide.
He was to pay for the miss just moments later as Kilmarnock opened the scoring after 25 minutes.
Rory McKenzie drove down the right wing and lashed a cross into the area where the retreating Hearts captain Wilson could only divert the ball past Jamie MacDonald for an unfortunate own goal.
The visitors were not behind for long however, and fittingly it was their liveliest player Carrick who brought them level.
The striker chased down a speculative high ball over the top and with Craig Samson and Lee Ashcroft hesitating, the young frontman nipped in to lift the ball over Samson into the unguarded goal for just his second goal of the season.
Kilmarnock captain Manuel Pascali should have perhaps put the home side in at the break ahead, but he just failed to connect with a vicious free-kick delivery from David Moberg Karlsson right in front of goal.
The home side did move ahead just four minutes into the second half however, Boyd out-muscling Jamie Hamill to get on the end of a loose ball he was second favourite for, and holding off the attentions of the Hearts midfielder to put a low left-foot effort past MacDonald for his 17th goal of the season.
The prolific striker had to wait just two more minutes for goal number 18, following some good work again by McKenzie who was now operating on the left.
His flick inside found Boyd in the area and the Scotland forward finished high into the roof of the net at the second attempt after his initial effort had been blocked.
Hearts breathed new life into the contest after 67 minutes when substitute Billy King ran down the right before picking out Nicholson in the area, who perfectly timed his arrival to slot past Samson.
Gardyne then crashed an effort off the crossbar at the other end and when the breaking ball was picked up by Jeroen Tesselaar, the left-back kept a cool head to pick out Gardyne making his way into the six-yard box.
He would not be denied on this occasion as he tapped home at the near-post to restore Kilmarnock's two-goal cushion after 71 minutes.
Boyd could have had his hat-trick moments later, but he was denied by the feet of MacDonald after running in behind the Hearts defence.
Hearts substitute Paul McCallum had a late header disallowed for offside, but there was to be no further scoring as Kilmarnock gave themselves some vital breathing space at the foot of the table.