St Mirren have not lost at home in their last eight outings, but with the worst scoring record in the league it was little surprise that genuine scoring chances were few and far between.
Both sides struggled to create chances, but it was St Mirren's superior delivery at set-pieces that eventually proved the difference between the two sides as Will Haining headed in from a corner.
St Mirren started brightly and had the better of the early chances.
Andy Dorman tested Alan Combe with a powerful shot after 11 minutes, although the keeper was more than equal to the challenge.
The Paisley side might be the lowest-scoring club in the SPL this season but the players were trying their best to rectify that and Billy Mehmet saw his 25-yard strike well-saved by Combe.
As the match went on, play gradually became more bogged down in midfield with real scoring chances few and far between.
Four minutes from half-time, Jim Hamilton was set up by Dorman before firing in a powerful right-foot shot which was comfortably stopped by Combe.
Kilmarnock's only genuine chance of the first half came seconds before the interval from a set-piece.
David Fernandez delivered a free-kick into the box and Grant Murray rose and headed at goal only for Mark Howard to pull off an excellent save a full stretch.
The second half started at a higher pace with the introduction of Ryan O'Leary and Mehdi Taouil bolstering the Kilmarnock side.
Jamie Hamill almost caught out Howard with a looping effort which hit the bar before luckily landing in the goalkeeper's hands.
Franco Miranda earned St Mirren a corner after seeing his close-range attempt tipped over the bar by Combe.
The home side looked most dangerous at set-pieces and nearly snatched the win from a corner in the dying seconds but Combe again did well to block John Potter's header.
The goal eventually came from a corner with an excellent delivery from Dorman headed in by Haining for his first goal for the club.