The home side had their manager Lee Clark sent to the stand and Motherwell took the lead thanks to a sublime chip from Lionel Ainsworth.
Mark McGhee's side doubled their advantage immediately after the interval with Marvin Johnson's header.
Killie pulled a goal back through Martin Smith's header, which resulted in a late if ultimately futile rally.
The first major moment of drama happened off the pitch with Clark's dismissal. It looked like it was for something he said to the fourth official after he was spoken to about leaving his technical area.
Motherwell had a great chance to score when Ainsworth crossed for Scott McDonald but the former Australia striker fired wide.
After an early curled effort from Soulemane Coulibaly went past, Kilmarnock struggled to create, though Stevie Smith's free-kick went just over.
Well almost took the lead in bizarre fashion when an attempted clearance from Miles Addison ricocheted off Craig Clay. The ball looked goal-bound but Jamie MacDonald pulled off a great save.
However, moments later Motherwell did take the lead with a moment of magic from Ainsworth. His pace took him clear of the Kilmarnock defence and, as MacDonald rushed out of his goal to close the angle, Ainsworth showed terrific composure to lob the keeper.
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After just 30 seconds of the second half Motherwell netted again. A great cross from Chris Cadden was headed home by Johnson and it suddenly looked bleak for the home side.
Kris Boyd immediately came off the bench and almost scored straight away, Craig Samson blocking. From the corner, Addison headed just wide.
Ainsworth should have made it 3-0 after he sprung the offside trap but his finish was poor and MacDonald gathered comfortably.
Samson made a good save from a low Boyd free-kick from 25 yards but Kilmarnock were struggling to create enough chances to get back into the game.
But suddenly that chance came. A cross from Greg Taylor found the head of substitute Smith and the midfielder flashed a header past Samson.
Kilmarnock were left flummoxed at the end as Coulibaly tangled with defender Ben Heneghan. It looked like a possible penalty but a free-kick was awarded to Motherwell, much to the anguish of the home fans.
Match ends, Kilmarnock 1, Motherwell 2.
Second Half ends, Kilmarnock 1, Motherwell 2.
Foul by Souleymane Coulibaly (Kilmarnock).
Stephen McManus (Motherwell) wins a free kick in the attacking half.
Ben Heneghan (Motherwell) is shown the yellow card for a bad foul.
Attempt saved. Steven Smith (Kilmarnock) right footed shot from outside the box is saved in the top left corner.
Substitution, Motherwell. Ross MacLean replaces Lionel Ainsworth.
Foul by Ben Heneghan (Motherwell).
Gary Dicker (Kilmarnock) wins a free kick in the attacking half.
Chris Cadden (Motherwell) wins a free kick in the defensive half.
Foul by Martin Smith (Kilmarnock).
Corner,  Kilmarnock. Conceded by Steven Hammell.
Goal!  Kilmarnock 1, Motherwell 2. Martin Smith (Kilmarnock) header from more than 35 yards to the top left corner. Assisted by Gary Dicker.
Lionel Ainsworth (Motherwell) wins a free kick in the attacking half.
Foul by Martin Smith (Kilmarnock).
Substitution, Kilmarnock. Martin Smith replaces Greg Kiltie.
Attempt saved. Kris Boyd (Kilmarnock) right footed shot from outside the box is saved in the top left corner.
Foul by Chris Cadden (Motherwell).
Rory McKenzie (Kilmarnock) wins a free kick in the attacking half.
Foul by Scott McDonald (Motherwell).
Kris Boyd (Kilmarnock) wins a free kick in the defensive half.
Corner,  Motherwell. Conceded by Jordan Jones.
Corner,  Kilmarnock. Conceded by Stephen McManus.
Corner,  Kilmarnock. Conceded by Stephen McManus.
Attempt saved. Kris Boyd (Kilmarnock) right footed shot from outside the box is saved in the top left corner.
Foul by Craig Clay (Motherwell).
Rory McKenzie (Kilmarnock) wins a free kick on the right wing.
Attempt saved. Lionel Ainsworth (Motherwell) right footed shot from very close range is saved in the top left corner.
Lionel Ainsworth (Motherwell) wins a free kick in the defensive half.
Foul by Steven Smith (Kilmarnock).
Foul by Richard Tait (Motherwell).
Jordan Jones (Kilmarnock) wins a free kick on the right wing.
Corner,  Motherwell. Conceded by William Boyle.
William Boyle (Kilmarnock) is shown the yellow card for a bad foul.
Substitution, Kilmarnock. Jordan Jones replaces Dean Hawkshaw.
Scott McDonald (Motherwell) wins a free kick in the attacking half.
Foul by Gary Dicker (Kilmarnock).
Substitution, Motherwell. Joe Chalmers replaces Carl McHugh because of an injury.
Richard Tait (Motherwell) wins a free kick in the attacking half.
Foul by Greg Kiltie (Kilmarnock).
Motherwell started their Premiership campaign with an away victory over Kilmarnock.