After a mediocre first half, the game came to life in the second period as Kilmarnock grabbed the win thanks to goals by Grant Murray and substitute Paul Di Giacomo.
With Robbie Neilson's testimonial just 24 hours away, Stephen Frail rested a number of players including captain Christophe Berra, who is one booking away from a suspension.
Neither side produced any real football of note in the first half with only one chance coming in the opening 45 minutes.
That opportunity fell to Hearts' Argentine Fernando Screpis who got on the end of an excellent cross from the stand-out player of the half Eggert Jonsson. However, Screpis could only fire his shot straight at Alan Combe in the Kilmarnock goal.
Kilmarnock did little to trouble Steve Banks in the Hearts goal. Allan Johnston sent a header well wide while Jamie Hamill's weak shot was easily covered by the experienced keeper.
The second half got off to a much brighter start as both sides looked to snatch a goal. Paul Dalglish tried to catch out Banks in the opening seconds of the second period with a 35-yard free-kick but his effort was off target.
Seconds later James Fowler bent a shot over the crossbar. Although Banks was never really troubled it was Kilmarnock's best chance of the match so far.
Hearts substitute Kestutis Ivaskevicius had his back-post header cleared off the line by Simon Ford. The ball fell straight to Screpis but he could not control his half-volley and fired over the bar from 30 yards out.
Killie substitute Di Giacomo put his own defence under pressure immediately after coming on to the pitch, giving the ball away three times in a minute. A mix-up between Combe and Murray almost led to an embarrassing own goal for the visitors.
It was Kilmarnock that grabbed the opening goal in the 74th minute when David Fernandez whipped a great ball into the six-yard box from a corner and ex-Hearts man Murray powered a header past Banks.
Fernandez was instrumental in the build-up to the second goal as he got the ball to Di Giacomo who clipped it home from the edge of the box.