Aberdeen had started as the stronger side but they never recovered from Davide Grassi's 25th-minute own goal. Alan Russell put the seal on the win for Killie in the 73rd minute.
The victory, which ended a run of six straight defeats and sees them move above St Mirren, came despite the loss of key players in all areas.
With midfielder Craig Bryson sidelined by a knee injury and on-loan Aberdeen striker Chris Maguire unavailable, Killie lost centre-back Frazer Wright in the opening two minutes.
Jimmy Calderwood, who had made four changes to his starting line-up by bringing in Garry Hay, Danny Invincibile, Mehdi Taouil and James Fowler, brought on Jamie Hamill at right-back and moved Tim Clancy inside.
However, Clancy had an impressive afternoon to deny Aberdeen despite their promising start. The Dons threatened with two early corners from Fraser Fyvie but Grassi headed well wide and Mark Kerr volleyed just over from 20 yards.
Sone Aluko, playing in a central role amid the absence of the suspended Steven MacLean, saw a deflected effort curl not far wide and he went closer midway through the half.
The Nigeria international collected Fyvie's pass with his back to goal 10 yards out before turning and firing a powerful shot that was parried brilliantly by Cammy Bell.
But the game soon changed when Grassi turned former Dons skipper Scott Severin's volley past Jamie Langfield and inside his near post.
Killie took control and could have added more before the break. Invincibile got underneath Taouil's arching cross and headed over, and Russell glanced Hamill's cross wide when Kevin Kyle was better placed.
Russell soon earned himself space to shoot from 20 yards and the ball was only held at the second attempt by Jamie Langfield.
Invincibile was replaced by Conor Sammon as the half entered injury-time and Bell raced off his line to block from Zander Diamond before the half-time whistle blew.
Aberdeen's frustration was displayed by Michael Paton when he swung his arm at Hamill after being dispossessed at the corner flag. Mike Tumilty showed the youngster a yellow card as the home fans bayed for red.
Paton soon made a more positive contribution, curling a powerful shot inches wide from 20 yards, but there was no sustained pressure from the visitors and Mark McGhee replaced midfielder Stuart Duff with striker Darren Mackie.
Kilmarnock went close again when Kyle headed on Severin's long throw but Langfield got down to hold Sammon's close-range header.
Charlie Mulgrew, Mackie and Fyvie were booked for Aberdeen as they struggled to get back into the game, and Clancy made a brilliant headed clearance to stop Grassi reaching Aluko's corner.
Paul Marshall replaced the injured Fyvie in the 73rd minute but his team fell further behind seconds later when Russell met Fowler's cross and looped a header over Langfield and into the top corner.
Kyle almost got on the scoresheet before his two-match suspension kicks in but Mulgrew cleared his header off the line following great wing play from Taouil.
Aberdeen had one chance to get back into the game when Mackie latched on to a long ball and lobbed over Bell's head but the goalkeeper backtracked and acrobatically pushed his effort over.
Killie ended the game well on top with Kyle twice trying his luck from long range and Langfield tipping over Sammon's effort.