Jamie Hamill drove home a penalty with the last kick of a poor first half and David Fernandez netted against his former side during a much livelier second period.
United sub Jon Daly had a penalty claim denied but Killie held on comfortably to knock the visitors off third spot.
The fortunes of both sides had transformed after Kilmarnock retained third place with victory against struggling United in late August.
Killie had lost five games on the trot, although three were against the Old Firm, while United had won eight games during their unbeaten run.
But the visitors struggled to break down a stubborn home side and Kilmarnock looked far more confident after Hamill had broken the stalemate.
Kilmarnock's fortunes were turning even before the game with defenders Garry Hay, Simon Ford and Hamill all returning from injury.
Fernandez also came back after being rested for the 3-0 defeat at Celtic with Conor Sammon replacing the injured Donovan Simmonds.
United, unchanged from the side that beat Hibernian on Wednesday, enjoyed decent spells of possession in the opening half but struggled to carve out a chance.
Kilmarnock goalkeeper Alan Combe handed his former club their only decent opportunity when he spilled Sean Dillon's cross.
Scott Robertson's shot was blocked in a busy penalty box and Craig Conway blasted the rebound over from 18 yards.
The home side sat deep for much of the half and United coped well with a couple of dangerous crosses from right-back Hamill, while Mehdi Taouil and Sammon were well off target with long-range efforts.
However, Taouil produced a moment of magic in injury time to burst into the left side of box and sidestep Morgaro Gomis, before being brought down by the United midfielder.
Referee Euan Norris pointed to the spot and Hamill drove his penalty kick into the middle of the net.
There was a far greater urgency to both teams when the game restarted.
Roy O'Donovan shot just wide from 20 yards after taking a long ball and his United strike partner Francisco Sandaza shot into the side netting after Lee Wilkie broke to feed him on the edge of the box.
Kilmarnock were getting more men forward when they had possession and Fernandez fired their second goal on the hour mark.
Sammon just missed Hay's cross from the left but James Fowler retrieved the ball, got to the line and cut it back for Fernandez to shoot high into the net from 12 yards.
United made a double change in the 66th minute with Danny Swanson and Jon Daly replacing O'Donovan and Willo Flood, while Willie Gibson came on for Kilmarnock midfielder Craig Bryson.
Gibson soon appealed for a penalty when Paul Dixon diverted his cross behind with his arm, but the corner almost yielded a third.
Fernandez and Taouil took it short and the cross fell for Manuel Pascali, who volleyed straight at Lukasz Zaluska.
United also had a strong penalty claim denied when Daly went down under the attention of Gibson after Robertson had set him up 10 yards out.
Sandaza then claimed Combe had brought him down just outside the area but Norris ruled the keeper's sliding challenge had won the ball.
Combe saved Gomis' long-range effort but the visitors could not sustain their pressure and Jim Jefferies rounded off a satisfying afternoon by bringing on Allan Russell for his home debut.
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