St Mirren snatched all-three points in a tepid affair at Love Street thanks to Will Haining's last-gasp winner.
Neither the Buddies nor Killie could break the deadlock during a flat SPL encounter at Love Street.
With both sides safe from relegation, the game had a real end-of-season feel about it with little goalmouth action.
Killie improved in the second half, with Danny Invincible going close, but Haining headed home Andy Dorman's 90th minute cross to steal a home win.
Both teams were sure of their SPL status for another season due to the travails of Gretna.
Unfortunately that was evident in a slow opening 10 minutes as both sets of players kept the ball on the deck and passed it around without urgency.
There was also barely a foul conceded in the opening period and the game already had the look of a pre-season friendly about it.
The first opportunity was carved out in the 11th minute when St Mirren's Craig Dargo slid the ball through to Andy Dorman.
But the midfielder's poked effort towards goal caused Killie goalkeeper Alan Combe little concern.
A more clear-cut chance arrived eight minutes later when David Barron's misjudgment of a lofted pass from Killie right-back Murray saw the ball drop into the path of Jamie Hamill 12 yards from goal.
MY SPORT: DEBATE
However the Kilmarnock midfielder dwelt on the opportunity too long and by the time he had got his shot away centre-half John Potter had made up ground to block his effort.
Billy Mehmet flashed a header just wide of Combe's right-hand post just after the midway point in the half.
But there was very little cutting edge to either side in the opening half hour.
Kilmarnock, missing a host of first-team regulars including Martyn Corrigan, Frazer Wright and Craig Bryson, were edging the contest thanks to the clever prompting in midfield from the recalled Allan Johnston.
St Mirren's most likely opening was down the left, Miranda getting forward from his new role at left-back to good effect in the 32nd minute.
It took fine handling from Combe to deal with his inviting cross.
Two minutes later Mehmet tried his luck with a 25-yard strike which required more safe handling from Combe.
St Mirren again tested Combe four minutes before the break, Jim Hamilton turning the ball towards goal from close range which Killie's keeper did well to push clear.
Two out of the last three meetings between the teams have produced no goals and it wasn't hard to see why.
Five minutes into the second half Stephen McGinn slid the ball through for Dargo to chase.
And the St Mirren striker stole a yard on his marker David Lilley as he looked poised to race clear on goal.
However the centre-half used all his experience to bustle the former Inverness forward off the ball and clear his lines - to howls of protest from the home fans who felt he had fouled their striker.
There was a definite improvement in the game at the start of the new half and Fernandez teed Danny Invincibile up for a powerful 55th-minute drive which Buddies keeper Mark Howard did well to push over the bar.
The introduction of the gifted playmaker Mehdi Taouil guaranteed some classy touches in the home midfield.
A wonderful turn and disguised pass by Taouil put Killie into a promising position on the hour mark - only for Hamill to slice the crucial final ball over the bar.
In the dying minutes Combe saved brilliantly from Potter when the St Mirren defender unleashed a powerful volley from just inside the box.
And with the game heading for a third goalless draw in the last four meetings between the sides, Haining threw himself at Dorman's superb cross to head past Combe and put St Mirren five points clear of Killie in the SPL.
St Mirren: Howard, Barron, Haining, Potter, Miranda, Mason, Dorman, McGinn (Kean 70), Dargo (Molloy 70), Hamilton (O'Donnell 90), Mehmet. Subs Not Used: Smith, Brittain, Brady, McCay. Goals: Haining 90.
Kilmarnock: Combe, Fowler, Lilley, Ford (O'Leary 46), Hay, Flannigan (Taouil 46), Johnston (Wales 73), Murray, Hamill, Fernandez, Invincibile. Subs Not Used: Rascle, Locke, Di Giacomo, Dalglish.
Booked: Hamill.
Att: 3,690
Ref: C Allan (Scotland).
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