Until the late decider it looked as though both teams would have to settle for a point from an evenly contested and entertaining match.
A first-half goal from Iain Vigurs should have set 'Well up for a win to enhance their chase for a Europa League spot but Rory McKenzie's second half equaliser brought the Rugby park side level and set up a grandstand finish.
Motherwell's James McFadden failed to recover from the hamstring he strained against Ross County, with teenage striker Craig Moore taking his place.
And as if the prospect of facing a Well side on a sensational home run was not daunting enough, Allan Johnston had to stop the hosts without his suspended captain and central defender Manual Pascali.
The Rugby Park side, only three points above the relegation play-off spot and without an away win since December, forced the first save after 13 minutes when Robbie Muirhead's thumping shot form 18 yards forced Gunnar Nielsen to save.
Midfielder Alexei Eremenko then threaded a through-ball for Rory McKenzie to chase but although he got in front of Stevie Hammell, Nielsen was smartly off his line to punch the ball away.
A trip on Moore at the edge of the Killie penalty area allowed Sutton drill in a free-kick which Samson spilled but Craig Reid was unable to force the loose ball inside the post.
The activity around the visitors' goal was increasing and Moore leapt the highest to meet a Vigurs free-kick - only to direct the ball over the goal.
Minutes later the Samson's goal had a narrow escape when Reid's header from Ainsworth's corner was sneaking inside the post until Muirhead cleared it off the line.
Motherwell deservedly opened the scoring five minutes from the interval. Vigurs first attempt from the edge of the box was blocked but when Moore rolled the ball back to the former Ross County man he hit a ferocious low drive which Samson could not keep out.
Three minutes later a terrific piece of footwork took Vigurs beyond two defenders only for him to drive his shot high into the side-netting.
Five minutes after the break Samson struggled to deal with a swerving shot from Moore but after the 'keeper palmed the ball out Lee Ashcroft mopped up the danger, booting the ball high over his own crossbar.
After the Killie defence failed to clear an Ainsworth corner, Keith Lasley returned the ball into a packed six-yard box but Sutton's glancing header sent the ball just outside the post.
On the hour mark Vitalijis Maksimenko broke upfield but after a 1-2 with Boyd the defender's shot was charged down by Stephen McManus. A minute later Eremenko's swerving cross was punched over the bar by Nielsen as the visitor's pushed for an equaliser.
And it duly arrived after 65 minutes. Jackson Irvine carried the ball towards the home penalty area unchallenged before playing the ball into the path of McKenzie who calmly steered his shot beyond the advancing goalkeeper to make it 1-1.
Stuart McCall immediately made a double substitution, bringing on Henri Anier and Jack Leitch and within minutes Well had penalty appeals waved aside as Anier fell inside the box as he attempted to get beyond Ashcroft.
Play raced to both ends of the pitch and in injury time, after Rory McKenzie had been carried off on a stretcher, Eremenko chipped onto the bar.
However, in the final move of the match Slater carried the ball towards the home box before drilling a shot across the diving Nielsen to give Kilmarnock a dramatic winner and all three points.