Killie were almost gifted the lead in only the third minute when Scott Paterson's clearance rebounded off one of his colleagues into the path of James Fowler. The full-back's shot beat Kenny Arthur but rebounded off the inside of the far post.
In a first half of little quality both sides squandered chances to open the scoring. David Lilley passed up Thistle's best chance in the 19th minute when he bounced his shot over the bar from Alex Burns' cross with Killie keeper Colin Meldrum stranded.
A probing run from Gary McDonald drew the visiting defence before he cleverly played in Gary McSwegan, but the veteran striker missed the gaping goal from 15 yards.
Kilmarnock took the lead on the stroke of half time when McSwegan nodded Alan Mahood's corner into the path of Peter Canero who shot low into the far corner of the net.
A poor clearance by Arthur gave McDonald a chance to extend Killie's lead eight minutes into the second half, but the youngster dallied too long in the box and could not get his shot away. The loose ball fell to McSwegan, but Arthur atoned for his mistake with a good smothering save.
Alan Archibald's set-piece deliveries were causing Meldrum and his defenders real problems and this looked to be Thistle's main chance of equalising, particularly when Killie lost Freddie Dindeleux to injury early in the second period.
The keeper had to pull off a magnificent save in injury time to deny Martin Hardie to ensure all three points stayed in Ayrshire.