Hearts owner Vladimir Romanov jetted in to see his side at Tynecastle for the first time since November 2008 and he was not disappointed after the Spaniard scored in the 32nd minute to give manager Jim Jefferies three points against his old employers.
The result leaves the Rugby Park outfit just one point ahead of basement side Falkirk, while Hearts are now just six behind city rivals Hibs in the race for European football.
The hosts were keen to impress banker Romanov from the start but it was hosts Kilmarnock who fashioned the first chance after just two minutes.
Chris Maguire evaded Andy Driver and whipped in a deep cross but Conor Sammon powered a header over from inside the six yard box.
The Gorgie outfit responded by creating an opening moments later but Christian Nade's toe-poked effort from 18-yards was blocked by the diving Cammy Bell.
Hearts enjoyed a sustained period of pressure as Santana had a stinging goalward drive deflected wide by the head of Nade.
The home side continued to enjoy the lion's share of possession but lacked creativity in the final third.
A piercing run from Santana, however, that saw the Spaniard play a one-two with Nade, left the winger with space to shoot but his left-footed effort from 18 yards was deflected wide for a corner.
Hearts were dealt a blow when Andy Driver, who has endured an injury-plagued season, pulled up chasing David Obua's pass on the half-hour mark and immediately signalled to the bench that he could not continue.
However, with Hearts down to 10 men as David Templeton prepared himself to come on, they took the lead in the 32nd minute.
Eggert Jonsson drove into the box and had a left-footed strike blocked by Kilmarnock captain Garry Hay. The ball fell kindly to Santana at the corner of the area and he flashed a low shot into the far corner past the stretching Bell.
Jefferies' side came close to doubling their advantage minutes later. Templeton and Ruben Palazuelos combined well on the left flank and the Spaniard crossed for Nade but the striker prodded the ball over.
Kilmarnock manager Jimmy Calderwood showed his disappointment at their first-half performance by making two changes at the break.
Ian Flannigan and Mark Burchill replaced Mehdi Taouil and Sammon.
Hearts began the second period looking to put the game beyond doubt and Larry Kingston was disappointed to hit a right-footed shot from outside the area well wide of target.
Kilmarnock striker Allan Russell became the first player in the match to be booked by referee Euan Norris after a late lunge on Lee Wallace as the Hearts defender cleared the ball.
Hearts goalkeeper Jamie MacDonald then produced a brilliant save to keep his side's lead intact in the 59th minute.
Manuel Pascali headed Flannigan's free-kick into the ground but the shot-stopper pushed the effort behind for a corner.
Hearts sub David Templeton responded by smashing a shot just inches over Bell's bar from distance after picking up a loose ball.
Hearts striker Nade missed another great chance to add a second in the 72nd minute. The ball fell for the Frenchman after Kingston's corner was flicked on by Marius Zaliukas but he whipped a shot wide from 10 yards.
A Flannigan corner was only partially cleared by goalkeeper MacDonald and Tim Clancy rifled an effort wide of goal from just outside the box.
The game swung from end to end as Hearts looked to consolidate their lead and Kilmarnock tried to restore parity.
Templeton was again involved for Hearts but he dragged a low shot wide from 18 yards.
Ian Black then somehow managed to loft the ball over the bar from just yards out from Kingston's corner.