There was almost a goal in the opening minutes when Motherwell's Brian McLean got his head to a Brian Kerr corner, but Steven Naismith was ideally positioned to clear off the line at his left-hand post. McLean could only manage to turn the rebound wide.
After eight minutes Killie took the lead with their first attack. Allan Johnston found himself in acres of space at the edge of the box, and his cross was tailor-made for Kris Boyd to head past Graeme Smith from six yards.
This stung Well who pushed to find an equaliser, which duly came after 23 minutes. A Kerr free- kick was headed into the six-yard box by Jim Hamilton for McDonald to toe-poke past Alan Combe from close range.
There were close things at either end, the best being a Simon Ford header for Killie that Smith had to be at full stretch for to turn over the bar for a corner.
Motherwell started the second half with a bang with the home side taking the lead eight minutes in. Hamilton was barged at the edge of the box and Kerr sent an unstoppable effort high into Combe's top right-hand corner.
With 15 minutes left it looked as thought Well had extended their lead when Hamilton got across Ford to toe-poke Shaun Fagan's cross goalwards, but his effort landed in the side netting.
Killie introduced Colin Nish, Stephen Murray and Gary Wales to bolster their attack, and with five minutes left Danny Invincible was unlucky to see his shot from the edge of the box deflected wide with Smith stranded.
In the final minute, after surviving a bit of a battering, Motherwell looked to have sealed it when Kerr saw another free-kick soar over the wall, this time to crash off the post. The home side were to pay for this in time added on. Boyd, in space only five yards from goal, had two shots blocked by Smith before forcing the ball home at the third attempt for an unlikely equaliser.