A second-half brace by Stephen Elliott earned Hearts three vital Scottish Premier League points at Rugby Park.
The visitors looked the sharper but went behind in 19 minutes when Rui Miguel placed the ball past Marian Kello from 18 yards for the opener.
Jim Jefferies made three substitutions for Hearts and one of those, Elliott, fired in from 12 yards past Cammy Bell.
Then, with four minutes to play, Elliott's shot squirmed past Bell to maintain Hearts' fine run of form.
Hearts started the brighter of the two sides, both of whom have compiled impressive runs in the Scottish Premier League this season, though the visitors were eight points ahead of Kilmarnock going into this match.
The big news at kick-off was that Kilmarnock's top scorer, 16-goal Conor Sammon, had turned down a move to Scunthorpe.
Having travelled south for transfer talks and returned to Ayrshire, manager Mixu Paatelainen decided it best to leave him on the bench.
In his place came the Portuguese Rui Miguel, who broke 19 minutes of Hearts domination to put Killie ahead with a well-placed shot.
The provider was Kilmarnock's playmaker Alexei Eremenko, who dispossessed Ian Black to set up his team-mate.
Hearts striker Kevin Kyle was a favourite with the fans at Rugby Park during his time there but injury prevented Hearts boss Jim Jefferies from fielding him on his return.
Injured, too, was Calum Elliot while Ryan Stevenson was a sub as Lee Wallace, David Obua and David Templeton were given starts.
Templeton played in a deeper role, Jefferies no doubt hoping he could use his pace to run at Killie's back line. That tactic left Obua in a lone striking role but, although Hearts got a good grip of the game in midfield for long periods, the Ugandan was isolated.
The Jambos' best chance of the first half came in 32 minutes when Bouzid flashed a header by the post, getting in front of his marker to knock it a fraction past from an inswinging Black corner.
In a keenly contested match, Hearts duo Adrian Mrowiec and Eggert Jonsson were booked in the opening period, the latter for crunching Liam Kelly, while Killie's Mohamadou Sissoko was shown yellow for bringing down Templeton as he raced towards goal.
Black had the chance to test Bell with the free-kick from Templeton's felling but his weak effort was deflected out for a corner.
Jefferies introduced Elliott for Arvydas Novikovas at half-time and his patience had expired by the hour mark when he brought on Gary Glen and Stevenson for Obua and Black respectively.
Such boldness paid off when former Preston striker Elliott levelled the match with 17 minutes remaining, a clinical finish into the corner of the net from 12 yards that gave Bell no chance.
Rui Miguel is congratulated by his team-mates for his opening goal
As the match hung in the balance, Bell made a mess of saving a shot from Elliott and was horrified as the ball crossed the line.
Killie had one late chance to take their unbeaten record to seven, but Kello made a terrific save from Garry Hay's powerful free-kick.
Prior to kick-off, Jefferies had said he would judge his team's ability to make a serious challenge in the SPL after the game at Rugby Park and matches against the Old Firm.
Three points from their trip to Ayrshire means there are 11 points between them in third place and Killie in fourth.
90:00+2:59 The referee brings the game to a close.
89:13 Stephen Elliott takes a shot. Save by Cameron Bell.
88:46 Alexei Eremenko takes the outswinging corner, Lee Wallace makes a clearance.
87:56 Free kick awarded for a foul by Ryan Stevenson on Mohamadou Sissoko. The free kick is delivered left-footed by Garry Hay from
right wing, Marian Kello makes a save.
86:00 GOAL - Stephen Elliott:Kilmarnock 1 - 2 Hearts Stephen Elliott scores a goal from just outside the penalty box to the bottom right corner of the goal. Kilmarnock 1-2 Hearts.
Correction - 84:30 Short corner taken by Ryan Stevenson from the left by-line.
84:30 Corner taken short by Ryan Stevenson.
83:51 The official flags Conor Sammon offside. Marian Kello restarts play with the free kick.
83:10 Substitution David Silva replaces James Fowler.
81:39 Inswinging corner taken right-footed by Alexei Eremenko, Marian Kello makes a save.
78:20 Inswinging corner taken by Ryan Stevenson, clearance by Frazer Wright. Outswinging corner taken right-footed by Ryan Stevenson,
clearance made by Manuel Pascali. Corner taken right-footed by Ryan Stevenson from the left by-line, save made by Cameron
77:38 The offside flag is raised against Stephen Elliott. Mohamadou Sissoko restarts play with the free kick.
76:22 Inswinging corner taken right-footed by Alexei Eremenko from the left by-line, Ismael Bouzid makes a clearance.
76:01 The ball is sent over by Conor Sammon, Frazer Wright takes a shot. Save made by Marian Kello.
75:24 Corner taken right-footed by Ryan Stevenson, Manuel Pascali makes a clearance.
72:23 Ismael Bouzid provided the assist for the goal.
72:23 GOAL - Stephen Elliott:Kilmarnock 1 - 1 Hearts Goal scored by Stephen Elliott from deep inside the penalty area to the bottom left corner of the goal. Kilmarnock 1-1 Hearts.
70:05 Free kick awarded for an unfair challenge on David Templeton by Tim Clancy. Free kick taken by Ruben Palazuelos.
69:18 Substitution Marinho Rui Miguel goes off and Conor Sammon comes on.
68:59 Effort from outside the area by Liam Kelly goes wide right of the goal.
67:06 Ryan Stevenson has an effort at goal from outside the box which goes wide right of the target.
65:24 Outswinging corner taken by Ryan Stevenson from the right by-line.
64:33 Substitution Billy Berntsson comes on in place of Mehdi Taouil.
62:08 Substitution Ryan Stevenson is brought on as a substitute for Ian Black.
61:42 Substitution David Obua leaves the field to be replaced by Gary Glen.
61:27 A cross is delivered by Lee Wallace, Manuel Pascali makes a clearance.
Correction - 59:17 Foul by Liam Kelly on Eggert Jonsson, free kick awarded. The free kick is delivered right-footed by Ian Black from right channel,
clearance made by Mehdi Taouil.
59:17 Unfair challenge on Eggert Jonsson by Liam Kelly results in a free kick. Free kick taken by Ian Black.
58:13 Foul by Lee Wallace on Tim Clancy, free kick awarded. Mehdi Taouil restarts play with the free kick.
57:35 Effort from 35 yards by Lee Wallace missed to the right of the net.
54:42 Free kick awarded for a foul by Marinho Rui Miguel on Ismael Bouzid. Free kick taken by Ismael Bouzid.
Correction - 53:58 The ball is swung over by Stephen Elliott.
53:58 The ball is crossed by Stephen Elliott.
45:01 The referee blows his whistle to start the second half.
45:01 Substitution Stephen Elliott on for Arvydas Novikovas.
45:00+1:21 The first half comes to an end.
45:00+0:47 Shot from just outside the box by Ian Black goes over the bar.
44:55 The assistant referee flags for offside against Marinho Rui Miguel. Direct free kick taken by Ismael Bouzid.
43:25 Free kick awarded for a foul by Eggert Jonsson on Liam Kelly. Garry Hay takes the free kick.
43:25 Booking Eggert Jonsson shown a yellow card.
42:08 Arvydas Novikovas produces a cross, clearance by James Fowler.
38:58 Foul by Ruben Palazuelos on Alexei Eremenko, free kick awarded. Garry Hay takes the direct free kick.
Correction - 36:51 Unfair challenge on David Templeton by Mohamadou Sissoko results in a free kick. Strike comes in from Ian Black from the free
kick, James Fowler gets a block in. Inswinging corner taken left-footed by Arvydas Novikovas.
36:51 Free kick awarded for an unfair challenge on David Templeton by Mohamadou Sissoko. Ian Black has an effort direct from the
free kick, James Fowler gets a block in. Inswinging corner taken from the right by-line by Arvydas Novikovas.
36:51 Booking Mohamadou Sissoko is shown a yellow card.
33:29 The assistant referee flags for offside against Marinho Rui Miguel. Marius Zaliukas takes the free kick.
32:57 The official flags Liam Kelly offside. Ismael Bouzid takes the free kick.
31:15 Corner taken right-footed by Ian Black to the near post, clearance by Manuel Pascali. Corner taken by Ian Black played to
the near post, Adrian Mrowiec has a headed effort at goal from close range which goes wide of the left-hand post.
29:15 Adrian Mrowiec challenges Manuel Pascali unfairly and gives away a free kick. Free kick taken by Garry Hay.
29:15 Booking Adrian Mrowiec is shown a yellow card.
27:21 Ruben Palazuelos gives away a free kick for an unfair challenge on Liam Kelly. Free kick crossed by Alexei Eremenko, Ruben
Palazuelos manages to make a clearance.
26:25 Effort from outside the area by Eggert Jonsson goes wide right of the goal.
25:44 Unfair challenge on Lee Wallace by Tim Clancy results in a free kick. The free kick is swung in right-footed by Ian Black,
clearance made by Garry Hay.
21:49 Arvydas Novikovas delivers the ball.
20:25 Foul by David Obua on Manuel Pascali, free kick awarded. Garry Hay takes the free kick.
18:15 Alexei Eremenko provided the assist for the goal.
18:15 GOAL - Rui Miguel:Kilmarnock 1 - 0 Hearts Marinho Rui Miguel finds the back of the net with a goal from just outside the area to the bottom right corner of the goal.
Kilmarnock 1-0 Hearts.
14:56 Free kick awarded for a foul by Marius Zaliukas on Marinho Rui Miguel. Strike comes in from Alexei Eremenko from the free
12:30 Effort on goal by Ruben Palazuelos from long distance goes over the crossbar.
10:34 Centre by Lee Wallace, clearance by Mohamadou Sissoko. Ian Black takes the inswinging corner, Tim Clancy makes a clearance.
6:07 Alexei Eremenko delivers the ball, clearance by Ismael Bouzid. Outswinging corner taken from the right by-line by Alexei Eremenko.
5:31 Unfair challenge on Marinho Rui Miguel by Ismael Bouzid results in a free kick. Alexei Eremenko restarts play with the free
4:30 The referee blows for offside. Mohamadou Sissoko takes the direct free kick.
3:12 James Fowler concedes a free kick for a foul on David Templeton. Marius Zaliukas takes the free kick.
0:47 Inswinging corner taken by Arvydas Novikovas from the right by-line, Mohamadou Sissoko makes a clearance.
0:32 The ball is swung over by David Obua, Frazer Wright gets a block in.
0:00 The game gets underway.
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