Richard Offiong claimed the only goal as Accies bundled home a corner in the first minute of the second period.
James McCarthy had struck the post in a first half dominated by Hamilton and Killie failed to get a shot on target despite some late pressure.
Hamilton are now nine points ahead of bottom club Inverness, and four points off the top six, after their fourth consecutive victory and clean sheet.
Killie suffered their seventh defeat in their last eight SPL games at Rugby Park and unlike many of the others, they can have no complaints over the result.
Hamilton included former Gretna striker Kenny Deuchar in their squad following his transfer from American side Real Salt Lake but they did not need his services as they sealed a well-deserved win.
They were strengthened by the return from suspension of skipper Alex Neil and Offiong, while on-loan Rangers youngster Jordan McMillan came in at right wing-back.
Referee Craig Thomson infuriated the home side in a scrappy opening by booking Frazer Wright for pulling back Offiong and then failing to speak to the Hamilton striker for a similar offence.
But Kilmarnock, who replaced the suspended David Fernandez with Danny Invincibile, soon had more pressing worries as Accies enjoyed some sustained pressure.
Offiong hooked the ball over the crossbar with his back to goal and Wright made a brilliant headed clearance from James McArthur's dangerous cross.
Kilmarnock were off target with too many passes and were grateful to Alan Combe for keeping them in the game before the break.
Combe dived at full length to tip wide Mark McLaughlin's deflected effort and then watched with relief as Craig Bryson's sliced clearance bounced on to the roof of the net following Paul McGowan's near-post corner.
James Fowler had been particularly sloppy in possession for the hosts and he almost gifted the visitors the opener when he gave the ball to McCarthy on the halfway line.
McCarthy broke quickly and fed Offiong, whose attempted chip was palmed away by Combe, and the Hamilton midfielder hit the post as he raced in for the rebound.
McGowan, McCarthy, McMillan and Killie midfielder Manuel Pascali all followed Wright into the book in the fiery first period.
Hamilton took less than a minute of the second half to take the lead when McGowan's near-post corner was scrambled home from close range.
Brian Easton headed the ball on and Offiong appeared to get the final touch as he and Simon Mensing followed in. The ball was at least a yard over the line before Garry Hay cleared and Thomson gave the goal after a short delay. Hamilton, with Trent McClenahan on for McMillan at half-time, kept pressing and Combe pushed away McGowan's 15-yard volley before the on-loan Celtic forward basted the rebound well over.
Killie brought on Donovan Simmonds, Gavin Skelton and Jamie Hamill before the halfway stage of the second period as Hamilton retained a firm grip on the game.
Invincibile and McGowan flashed shots just wide from long range at either end before Combe pulled off another stop from McLaughlin following a set-piece.
The hosts pinned Hamilton back for much of the final quarter but Tomas Cerny's only moment of concern came when his defender Martin Canning dummied a poor cross from Mehdi Taouil, and he got down well to hold the ball.
Kilmarnock's poor display was summed up when Skelton, a 64th-minute substitute, was named the sponsors' man of the match.