Stuart McCall's men were crushed 4-0 at home by Dundee United a couple of weeks ago but clearly used their time off well and put up a composed display that got its just rewards in the second half.
Kilmarnock set the early pace and created the first real chance when Chris Johnston won a free-kick and Sammy Clingan put in a delicious cross but Manuel Pascali could only head straight at Gunnar Nielsen.
But Motherwell soon found their rhythm with Craig Moore shooting just over the bar and Iain Vigurs failing to get enough on a James McFadden cross to test Craig Samson in the Killie goal.
Had Moore brought his shooting boots, 'Well could have led 3-0 inside the opening 30 minutes but two more golden chances were passed up by the young striker.
Samson produced a superb save to keep out John Sutton's powerful header and the busy Moore had another effort deflected wide, but visiting keeper Nielsen had to be alert to deny Kris Boyd what would have been an undeserved opener for Kilmarnock.
Moore played provider for Lionel Ainsworth just after the break but the winger dragged his shot wide, but Motherwell finally took the lead on 55 when Vigurs put over a cross and Sutton's diving header crept past Samson.
Killie responded quickly and almost levelled moments later when Michael Gardyne tested Nielsen's reflexes and no-one managed to get on the end of a wicked Craig Slater cross.
Boyd was left kicking himself with 25 minutes remaining, heading a deep cross over the bar from six yards when he would normally have backed himself to score.
The home side continued to press and sub Rory McKenzie fired a shot just wide of goal before Pascali headed a corner straight at a suddenly busy Nielsen.
But the points were settled in the 89th minute when sub Anier, who had replaced the luckless Moore 10 minutes earlier, spun past Pascali and toe-poked the ball past Samson.
The result lifts Motherwell above Aberdeen into third place and leaves Kilmarnock stuck in the relegation play-off place.