Any luxury Jim Jefferies enjoyed in naming an unchanged team lasted only two minutes as he was forced into an early substitution, when Paul di Giacomo received a nasty kick in the face from Stephen Craigan.
The visitors took the early lead following excellent work tight on the byline by Scott McDonald, who turned Garry Hay inside out before firing low across the face of goal for Richie Foran to stab home from two yards.
Well went two up in the 20th minute after desperate Killie defending. Keeper Graeme Smith should have taken command, but he allowed a deep cross to bounce and young Darren Smith took possession.
He fed the ball out wide and there were no challenges from Killie players as it was played back in to Jim Paterson, whose weak right-footed shot was deflected into the net.
It took a moment of brilliance from Steven Naismith to bring Killie back into the game seven minutes before the break. He picked the ball up on halfway and shrugged off Brian Kerr's challenge before advancing to the edge of the box and rifling a thunderous 25-yarder into the roof of the net.
Motherwell were reduced to ten men ten minutes into the second half when Paterson was shown his second yellow for time wasting as he dithered over a throw-in.
Disappointing Killie rarely looked like scoring the equaliser thanks to stubborn defending from Mark Reynolds and Craigan and their keeper had only one save to make when the ball bounced off Colin Nish from a Hay corner, but Graeme Smith flopped onto the line to grab safely.
In a bizarre finale Killie's Hay and Well's David Clarkson were both red-carded after they clashed.