The visitors were targeting a fourth win in five games, but goals from Paul Hanlon, Paul Cairney and Lewis Stevenson spoiled Killie's run and kept Hibs in touch with the Scottish Premiership top six.
Killie keeper Craig Samson kept out a shot from Jason Cummings in the early stages, but he could not prevent Hanlon (12) from nodding home a cross by Cairney.
Hibs nearly doubled their lead soon afterwards as Jordan Foster headed wide and James Collins fired past the post from close range.
But the visitors finished the half strongly and Michael Gardyne went close with two shots from outside the box.
Samson was forced into action again after the break as he kept out Stevenson's shot and the Hibs midfielder then drove the ball narrowly wide of the target.
But the hosts would not be denied and Cairney (76) rifled the ball into the bottom corner before Stevenson wrapped up the win with a low shot past Samson.