The former Celtic midfielder opened the scoring before the break before setting up Craig Curran for the second on the hour mark.
Lee Ashcroft netted a late consolation for the visitors but it was County who deservedly held on to claim another vital three points.
The win made it 16 points out of 18 for the Dingwal side while also ending Kilmarnock’s run of seven games without defeat.
In an end-to-an start, Gardyne twice went close during the opening quarter of an hour, first heading wide and then having a close range effort saved by Craig Sampson.
Scott Boyd fired narrowly over and Josh Magennis saw a goalbound effort blocked for the visitors before County opened the scoring midway through the first half when Liam Boyce glanced a header into the path of Gardyne who crashed the ball home from 15 yards.
As Kilmarnock chased an equaliser before the break, Darryl Westlake fired wide from just outside the box on 41.
However, it was County who continued to hold sway during the early exchanges of the second half and were duly rewarded on 58 when Curran located the bottom left-hand corner after latching on to Gardyne’s assist.
After being outplayed for the opening 75 minutes, Kilmarnock did their best to make a game of it during the latter stages.
First, Magennis headed inches wide before substitute Greg Kiltie struck a post, with Lee Miller unable to convert the rebound.
Miller and Manuel Pascali had other efforts before Ashcroft pulled a goal back on 88 when he stooped to head home Paul Cairney’s free-kick.
However, it was too little, too late and all but ends Killie’s chances of reaching the top six before the split while County edge closer to safety.