Kilmarnock made a bright start to the game as Motherwell's reshaped midfield, with Alex Burns in for Phil O'Donnell, struggled to get a grip of the game.
It was therefore a surprise when Motherwell took the lead after 15 minutes. Derek Adams bent a free-kick from the left and it was powerfully headed past the keeper by Paul Quinn for his first senior goal.
Motherwell dominated the remainder of the first half without adding to their tally.
This was despite good efforts from David Clarkson, Keith Lasley and the lively Scott McDonald. But Motherwell could never settle on the lead as Kilmarnock was constantly snapping at their heals.
Kilmarnock also started the second half the brighter of the two sides and wasted a good opportunity when awarded a free-kick at the edge of the box, but Kris Boyd's shot was blocked by Burns.
As the half wore on, Killie pressed for the equaliser without ever looking like troubling their former goalkeeper Gordon Marshall.
Their only real effort at the keeper came from a Gary Locke header that was easily saved.
Motherwell always looked likely to add to their lead as a result of Kilmarnock committing so many bodies forward.
The best two chances fell to Motherwell with an Adams shot sliding just wide of the far post. This was followed by a Burns cross which was cut out by Garry Hay as McDonald waited to pounce.
In the end Motherwell withstood the aerial barrage to keep their first home, clean sheet of the season and secure all three points that pushed them back into the top six.