Preston had started well at Deepdale as they looked to record a first league win in 14 games, but it was the visitors who opened the scoring through Kilkenny's fine strike.
Paynter then doubled the advantage and Iain Hume's goal was not enough to help Preston secure a point.
The win moves Leeds above Nottingham Forest and they now lie just three points short of an automatic promotion place.
Preston are now 13 points adrift of safety and are in need of a miracle if they are to retain their Championship status.
Preston were boosted by the availability of keeper Andy Lonergan and defender Craig Morgan, who missed the draw with Norwich with a stomach bug.
They were also able to include on-loan Bolton man Ricardo Gardner while Leeds had their own loan signing, Aston Villa's Barry Bannan, on the bench.
Despite their precarious position Preston almost made a dream start as Keith Treacy's ferocious strike from the edge of the Leeds box cannoned back off the crossbar with Kasper Schmeichel well beaten.
Hume then fired over from distance as North End raced out of the traps.
Striker Chris Brown, who grabbed his first goal of the season against Norwich at the weekend, also went close but Schmeichel was able to gather his header.
Leeds captain Jonny Howson blazed over the bar on a rare foray forward for the play-off hopefuls but the hosts continued to look the more likely.
Schmeichel made an athletic save to deny a low Eddie Johnson drive before Gradel forced Lonergan to do likewise for Phil Brown's men.
Preston may have looked the more likely to grab an opener but they were stunned when the visitors took the lead against the run of play.
The ball fell to Kilkenny 20 yards out and he hammered the ball beyond Lonergan into the top right-hand corner in the 29th minute.
Paynter's shot was well blocked by Sean St Ledger as Leeds pressed for a second before Brown missed a glorious chance to level eight minutes before the break.
Hume's cross found the striker six yards out, but he somehow failed to hit the target.
Treacy again went close from distance upon the resumption but Schmeichel was again equal to the task.
Simon Grayson's men now looked far more assured and the lively Gradel was twice narrowly off target from the edge of the box, but Paynter's effort a few minutes later was on target and saw Leeds double their advantage in the 57th minute.
But Preston showed great spirit to respond just six minutes later.
Treacy picked out Hume and the former Barnsley man smashed the ball into the top corner to give the home side hope of salvaging something from the game.
Paynter could only hit the bar from close range from Gradel's cross, before the winger himself wasted a good chance by heading straight at Lonergan.
Bannan made his debut as a substitute and Preston pushed forward late on in search of a leveller but Leeds held out for the three points.
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