Mickael Antoine-Curier got the only goal of the game three minutes from half-time at Rugby Park, deserved reward for a strong first 45 minutes from the visitors.
Darian Mackinnon looked dangerous early on for Hamilton, having a shot deflected behind for a corner and then drawing a save from Craig Samson with a long-range effort.
The in-form Accies continued to look the more dangerous of the two sides and Michael Devlin headed just over the bar before Samson saved really well from Antoine-Curier, although the forward had already been ruled offside.
And Hamilton secured a lead which they thoroughly merited when Ali Crawford sent over a corner and Antoine-Curier got up well at the near post to score with a bullet header.
Killie were kept very quiet in the first half but showed more intent after the interval and Rabiu Ibrahim let fly from 25 yards, Hamilton keeper Kevin Cuthbert doing well to tip the shot over the crossbar.
However, Antoine-Curier then got on the end of another corner for the visitors, only for his header to be off-target on this occasion.
The hosts brought Paul Heffernan off the bench and he was picked out by William Gros but headed straight at Cuthbert, before Gros himself nodded a Rory McKenzie corner wide.
Gros was in the thick of the action in the closing stages but had a shot deflected out for a corner and then met the subsequent set-piece, only for a Hamilton defender to clear off the line.
Kyle Jacobs was the next Kilmarnock player to test Cuthbert but the keeper easily caught his long range shot and the Accies also had late chances to double their lead, Andy Ryan hitting the side netting in stoppage time.