Fraser Taylor's maiden goal for St Mirren helped them to their first league win at Rugby Park in over 13 years - heaping more pressure on struggling Kilmarnock.
Saints passed up numerous opportunities during the first half but found themselves under pressure late on as Neil McCann's men chased an equaliser.
The Killie boss made three changes to his defence in response to their 4-0 home defeat to Dundee United last weekend.
Having conceded 13 goals in their opening three Premiership games, it was perhaps little surprise that McCann opted for a change of formation in an attempt to shore up his leaky backline.
Moving away from a back four to a 3-5-2, McCann brought in Erik Ring, George Stanger and Johnly Yfeko. The injured Robbie Deas and Nicky Clescenco dropped out, while Jonathan Meier was named on the bench.
There was one switch for the Buddies, with Taylor making his first league start of the new campaign in place of Samuel Ramos.
Joe Hugill almost found himself through on goal in the third minute when Max Stryjek's long pass caught out the St Mirren backline - but the striker was unable to bring the ball under control.
Killie were behind a minute later when the visitors pounced on some slack play in the middle of the park, launching a quick counter which ended with Taylor sweeping Nikolas Agrafiotis' pass into the bottom corner.
There was a nervousness around the home supporters any time Saints entered the final third.
On 13 minutes, an intricate passing move cut open the Killie defence, though Calvin Ramsay's strike deflected off Yfeko and against the right-hand post.
Just after the half-hour mark, another smart block from Yfeko prevented Chris Mochrie from doubling Saints' lead.
The resulting corner also caused problems in the home defence, though this time Declan John was unable to take advantage as he slashed well wide of the target.
Paul Nsio was next to try his luck for Craig McLeish's side, sending an angled effort high and wide in the final minute of the first half.
Following another abject display from his team, McCann made a triple substitution at half-time. Jamie Brandon, Aaron Tshibola and Djenairo Daniels came on for Tyreece John-Jules, Yfeko and Ring.
Jacob Chapman was tested for the first time in the 47th minute when he batted away Tom Lowery's free-kick.
On the hour mark, the St Mirren keeper comfortably gathered Michael Schjonning-Larsen's low drive as the driving rain continued to batter Rugby Park.
With the home side pressing for an equaliser, they were leaving big gaps at the back which St Mirren looked to exploit at every opportunity.
A well-worked counter saw Jake Young combine well with Nsio, but the forward couldn't quite adjust his feet in order to get a shot away.
Killie responded quickly at the other end with a promising attack of their own. However, Daniels was unable to profit as Chapman raced from his goal, with the substitute instead sending the ball into the side netting.
With 17 minutes remaining, a brave block by Alex Gogic kept out Rory McKenzie's goal-bound volley.
In the final minute, Cathal McCarthy nodded into the side-netting from close range after finding room inside the box at a corner.
Despite their improvements in the second half, chances were limited for Killie, ensuring Saints picked up a rare three points in Ayrshire.