The price of a bottom six finish was evident as Killie's lowest crowd of the season saw them keep only their second clean sheet of the season.
The match lumbered through the first quarter, but some vintage wing play from Killie's Stevie Murray brought it to life in the 22nd minute when he skipped past two defenders before squaring to Craig Dargo, who shuttled the ball to Rhian Dodds on the edge of the area.
The midfielder struck his shot well, but not beyond the outstretched hand of Daniel Andersson.
The home side took the lead six minutes later with a simple but well executed goal.
Freddy Dindeleux strode out of defence and fired a long pass through the middle, sending Kris Boyd through with only Colin Murdock to beat. The striker rolled around the centre-back easily and fired an unstoppable shot into the net.
Gary Caldwell looked anything but an international defender and almost gifted two goals in the closing minutes of the half.
First when he played a pass-back straight to Boyd in the penalty area. He selfishly passed to Dargo, but he was forced wide and could only shoot into the sidenetting.
Then, on the stroke of half-time, he missed a clearing header which sent Boyd clear again, but this time Andersson was able to save with his feet.
Hibs were posing no threat to Kilmarnock who came close to adding a second in the 68th minute. Eric Skora's deep corner found Boyd, but his header couldn't beat the far post.
Skora was the architect again eight minutes later with a great pass which sent Murray scuttling into the box. He cut back on to his weaker right foot and aimed a chip for the far corner which Andersson did well to tip away.
Killie keeper Colin Meldrum was a virtual spectator, but pulled out a great save after Danny Invincibile's mistake gave Derek Riordan a sight of goal and he hit a stunning volley which Meldrum dived to his left to parry.
Killie secured the win in the 84th minute. Invincibile's clearance gave Boyd another chance to run in on goal.
He was strong enough to hold off Murdock and gave Andersson no chance with a powerful low finish.