Killie's team selection even had an eye on next season as Jim Jeffries made seven changes to his side to prevent injuries and suspension.
As luck would have it he was forced to make two further changes in the early stages of the first half, when Grant Murray and Manuel Pascali had to be replaced after a clash of heads.
Despite Motherwell having the bulk of possession it was Killie who should have opened the scoring after 16 minutes.
Mehdi Taouil cut in off the left wing but he failed to pick out Danny Invincibile who was standing in acres of space.
Thankfully for the visitors, ten minutes later, Taouil did manage to find Invincibile in space once again and the Australian made no mistake as he hammered high past debutant keeper Artur Krysiak.
Motherwell should have been level ten minutes after the restart, but Brian McLean was unlucky to see his glancing header bounce clear off the crossbar.
Minutes later another Jim O'Brien corner caused panic in the Killie six-yard box, but Cillian Sheridan could only manage to head wide despite being unmarked.
Sheridan was then unlucky two minutes later when a reverse pass from Stephen Hughes gave him a chance form a narrow angle, but Killie keeper Cameron Bell got down to block well.
The home side finally found an equaliser with only ten minutes left when David Clarkson robbed Tim Clancy on the right before heading for the byline. He looked up and picked out McLean who sidefooted home from eight yards out.
Killie sealed a win thanks to some outrageous skill from David Fernandez, his backheel flick took out three Motherwell defenders and released Taouil.
He fooled the Well defence with a couple of step-overs before rifling high past Krysiak.