Steven Thompson scored twice from the spot to add to Sean Kelly and Kieran Sadlier’s first-half goals as the bottom-placed team hauled themselves to within seven points of Motherwell, who lost 2-0 at Hamilton on Friday evening.
St Mirren manager Gary Teale was without suspended pair Jim Goodwin and Viktor Genev, while Marc McAusland was ruled out with a knee problem and midfielder John McGinn watched on from the stands on crutches.
Teenager Jack Baird came in along with fellow-midfielders Sadlier and James Dayton, while forward Thomas Reilly and full-back Jeroen Tesselaar were also included.
Killie made four changes – with skipper Manuel Pascali returning alongside Ross Barbour, Chris Johnston and Nathan Eccleston.
Reilly had the best chance early on but headed over the visitors’ crossbar before Kelly opened the scoring with a left-footed shot from the centre of the penalty area in the eighth minute.
Stephen Mallan, Baird and Thompson all went close as the hosts took control, while Kilmarnock were forced to replace injured Eccleston with Lee Miller.
Pascali’s header drew the first save of the game out of Mark Ridgers in the 32nd minute but just 60 seconds later Sadlier justified his place in St Mirren’s starting XI by doubling the lead with a fine header.
Kilmarnock hit back after the break when Josh Magennis found the target with a left-footed shot from outside the box in the 57th minute.
However, Thompson restored St Mirren’s lead from the penalty spot just four minutes later after Alexei Eremenko had handled in the box.
Magennis was denied a second by a save from Ridgers and shortly after Kilmarnock conceded another penalty after Pascali fouled Dayton in the box.
Thompson (64) scored his second spot-kick inside 10 minutes to extend the lead and open up breathing space for the Buddies.
Magennis was denied again twice and hit the upright in a lively ending to the match which also Mallan force a save from Craig Samson before rattling the crossbar.