Dennis Wyness' brilliant pass to Andy Dorman was the deciding factor as the Saints continued to pull themselves away from the foot of the SPL table.
The first half was full of honest intent without either side dominating play or creating chances.
Kilmarnock had David Fernandez available after suspension and Jim Jefferies fielded an attacking 3-4-3 formation which allowed the Spaniard a free role, but too often the one touch movements were crowded out.
During a brief period of sustained Killie pressure, it took two determined blocks from the Buddies defenders to keep out solid hits from Donovan Simmonds and Alan Russell.
The Saints took the lead in the 38th minute with the best play of the half.
Wyness' fabulous flick on the edge of the box bisected Killie's last two defenders perfectly for Dorman to simply fire the ball low in the far corner from 15 yards.
Killie central defender Fraser Wright was replaced immediately due a hamstring strain by Craig Bryson, but even fully fit he could not have prevented the slick strike.
St Mirren clearly set out to frustrate Kilmarnock in the second half, even leaving them waiting on the pitch for a full two minutes in the rain before leaving the warmth of the dressing room.
They then proceeded to delay the game whenever possible in a tactic that didn't win any friends but secured vital points.
In truth they didn't have to try too hard to frustrate Killie as they were doing a fine job by themselves with their poor passing.
Gus MacPherson's men did create the first chance of the second half when evergreen Jim Hamilton's header found Dorman, but he shot straight at Combe.
Full-back Jack Ross got the visiting fans out of their seat when his well-struck shot fizzed across the damp turf and only a lick of paint wide of the far post.
The home side were roused in the 74th minute when they were denied a strong penalty appeal when the ball clearly struck John Potter's outstretched arm, but referee Stevie O'Reilly waved the claims aside.
Saints had the chance to wrap up the points in the 89th minute on the break.
Substitute Billy Mehmet had the first go but was blocked by the diving Grant Murray.
The ball broke to Garry Brady, who hit a lovely curling shot from 20 yards which beat the keeper but hit the post.
It rebounded to Mehmet but Combe recovered well to save with his legs but it did not affect the outcome of the match.