Jim Jefferies' defensive injury list had cleared up sufficiently to allow Simon Ford and Garry Hay to start the match, and the home side looked much more confident as a result.
The first half was even and entertaining enough, although it took until stoppage time to see any goal threat, when Kilmarnock were awarded a penalty.
Killie's Moroccan midfielder Mehdi Taouil danced his way to the left edge of the box and enticed Morgaro Gomis into a careless tackle which took his feet away.
Jamie Hamill refused to allow anyone else to take the spot-kick and saved himself a rollicking from his team-mates as he shot the ball low and straight beyond Lukasz Zaluska who had committed to a dive to his left.
Roy O'Donovan had United's first real attempt at goal in the 50th minute when he did well to hold off Fraser Wright and fired in a good 25-yard shot which drifted wide.
Lee Wilkie set up United's next attack in the 58th minute when he stepped in to halt a Kilmarnock break, and slid a first-time pass to Francisco Sandaza who weaved his way into a shooting chance but only found the side-netting.
Kilmarnock stretched their lead two minutes later. The danger seemed to have passed when Hay's cross flew over striker Conor Sammon's head, but James Fowler collected the loose ball and skinned the full-back, Paul Dixon, and intelligently cut the ball back to David Fernandez who had the easy job of stabbing the ball home.
Both sides had strong penalty appeals turned down in the space of two minutes as United pushed men forward in the last quarter.
A whipped Fernandez cross in the 69th minute almost brought a third Killie goal, but Zaluska was well positioned to claim Manuel Pascali's instinctive volley on the line.
United boss Craig Levein pushed Wilkie into the attack for the last ten minutes, but Alan Combe wasn't forced into a save by a very disappointing United performance until the last minute of stoppage time when he was able to catch Gomis' long-range curler.