A Kevin Kyle double had the home side on easy street until a late Dennis Wyness goal gave Saints a sniff of salvation.
As one might expect from a match between a team in the thick of the relegation battle and one in the periphery, it was the team deep in the dog fight that came out with the greater intent.
St Mirren dominated the first ten minutes, but continually misjudged the strength of the wind behind them and several moves fizzled out with the ball rolling harmlessly past.
Saints cause a few home hearts to skip beats in that time with a couple of crosses that bent close to the Killie goal, but Alan Combe looked in control on both occasions. Andy Dorman also hit a rasping 30-yard shot but it flew inches over.
Killie struggled to trouble the St Mirren goal, but they have the country's in-form striker in Kevin Kyle and he needed only one chance to put his side in front with his fifth goal in three games.
It came in the 23rd minute and originated from a sloppy clearance by John Potter. The experienced defender played the ball straight to Mehdi Taouil, who chipped the ball into the danger area where Kyle galloped in on it and powered a header low past the helpless Mark Howard.
St Mirren came out for the second half knowing that this was a match they couldn't afford to lose, but their early impetus was punctured by Kyle's second goal three minutes after the break.
The architect this time was Willie Gibson who held off Potter on the left and teed up Kyle who made no mistake from eight yards.
Dorman attempted to drag Saints back into the match with an audacious shot from a tight angle, but Combe cleared spectacularly.
Taouil had the chance to wrap up the points for Kilmarnock in the 73rd minute when good play between Gibson and Garry Hay gave him a clear sight of goal eight yards out, but a desperate block from Will Haining sent the ball wide.
The Buddies threw on Craig Dargo to make a front three, but they could find no way past the Killie rearguard where David Lilley was immense.
Dargo set up a grandstand finale when swept a loose ball home after the Killie defence had failed to clear a Dorman shot in the 90th minute, and they thought they had found a vital equaliser in injury time, only for the referee to award Killie a free-kick when a corner had been headed home.