Thistle came into this match riding on a crest of a rare wave after scoring ten goals in a week bringing them back into touching distance of the SPL pack.
Killie had taken only one point from the previous seven league matches, and even more worryingly, had scored only one goal in their last five home games - and that was a penalty.
That lack of confidence in front of goal could go some way to explaining Gary McSwegan's dreadful early effort which skewed parallel to goal and into touch from ten yards out.
The midfield was an unseemly mess, but Kilmarnock began to take the upper hand in the battle of attrition, but could not force a shot on target.
Eric Skora's free-kicks and corners created panic in the Thistle defence, with McSwegan just failing to reach a low cross and Adrian Madaschi heading narrowly past his own post from another teaser.
Five minutes before the break, Stephen Murray popped up on the right wing and released the over-lapping Rhian Dodds whose right-footed pile-driver brought the best out of Kenny Arthur.
Jim Jefferies replaced Dodds with striker Kris Boyd at half-time, but as so often at Rugby Park, it was the away side that scored first.
It was a scrappy goal, in keeping with the quality of the match. Gerry Britton's snap-shot was half-blocked by Barry McLaughlin and the ball broke to Stephane Bonnes whose stabbed shot bounced off the keeper's body before bumbling over the line.
Thistle have a habit this year off giving up winning positions and within five minutes they found themselves behind.
Killie's equaliser came from David Lilley as the defender, signed in January from Thistle, fly-hacked the ball home after Skora's teasing free-kick was nodded back by Boyd.
It was Boyd who put Kilmarnock ahead in the 57th minute when he powered a header home at the far post from another Skora delivery.
McSwegan and Boyd both passed up golden chances to stretch the lead as they had fresh air swipes from point-blank range, before Arthur produced a great save to touch Boyd's deflected shot round the post.