The centre-half glanced on Andy Dorman's free-kick in the 90th minute to give Gus McPherson's side all three points in a tepid match of few highlights and even fewer goalscoring opportunities.
Killie midfielder Jamie Hamill had Jim Jefferies' side's only genuine clear-cut chance but he dwelt too long on the ball in the box and his shot was blocked by St Mirren centre-half John Potter.
With both teams having their SPL status guaranteed for another season due to the travails of Gretna, there was no real pressure on the players.
That scenario was clearly evident in the opening 10 minutes as both sets of players tried to pass their way out of trouble whereas in similar situations during matches of more importance they would have merely sought to clear their lines.
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 Craig Dargo slid the ball through to 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 misjudgement of a lofted pass from Killie right-back Grant Murray - drafted in to replace Tim Clancy after the youngster was injured in the draw against Gretna - saw the ball drop into the path of Hamill 12 yards from goal.
However the Kilmarnock midfielder dwelt on the opportunity too long and by the time he got his shot away centre-half 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.
The former Hearts and Rangers schemer was back in the side at the expense of striker Paul Dalglish as Jefferies adopted a 4-5-1 formation with Spanish front man David Fernandez at its apex.
St Mirren's most likely opening was down the left with Franco Miranda - recalled to the side in place of Ryan McCay in the only change to the side which defeated Falkirk last week - getting forward from his new role at left-back to good effect.
Indeed in the 32nd minute he darted down the flank and produced an inviting cross which Combe dealt with efficiently as St Mirren players lurked in search of a goalkeeping mistake.
Two minutes later Mehmet tried his luck with a 25-yard strike which required more safe handling from Combe.
It was hardly an onslaught from the home side but they did again test 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 as the half ended scoreless.
Jefferies made two substitutions at the interval, Iain Flannigan making way for gifted playmaker Mehdi Taouil and Simon Ford being replaced by Ryan O'Leary.
Five minutes into the new 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 Killie 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 Taouil guaranteed some classy touches and one wonderful turn and disguised pass put Killie into a promising position on the hour mark - only for Hamill to slice the crucial final ball over the bar.
With 20 minutes remaining, McPherson made his first substitutions, taking off McGinn and replacing him with Craig Molloy and sending on Stewart Kean in place of Dargo.
Jefferies played his final card two minutes later, introducing Gary Wales at the expense of Johnston - probably the game's best player to that point.
After hinting at signs of a more positive second period, the game was now in danger of petering out as neither side found themselves able to keep possession.
A typical example of the profligate football came in the 85th minute when Fernandez set Invincibile racing clear down the left but the Australian's side-footed effort lacked power and conviction.
The best moment of the match followed two minutes later when Potter unleashed a terrific right-footed drive towards the left-hand corner of the goal - only to see Combe palm the ball away to safety.
Seconds from the end the deadlock was finally broken as Haining headed Dorman's free-kick into the same corner of the net that his centre-back partner Potter had tried to find as St Mirren claimed three points from an uninspiring match.
Sandy's Match Pic's are HERE
