With Gold Coast leading by three points at Marvel Stadium, young Suns defender Mac Andrew was penalised for an off-the-ball hold on Saints spearhead Max King as the pair jostled close to goal.
With less than three minutes to go, much to Andrew's dismay, King converted from point-blank range and St Kilda held on for a 7.9 (51) to 7.6 (48) win in front of 17,992 fans on Saturday night.
It spared St Kilda's blushes, mere minutes after Suns skipper Touk Miller escaped Marcus Windhager's tag to give the visitors the lead for the first time after the Saints had dominated much of the game without reward.
Damien Hardwick's Suns (7-6) had the opportunity to cement themselves in the top eight - and sit outside the top four on percentage alone - with a victory, but they will instead drop out of the eight by the round's end.
Ross Lyon's St Kilda (5-8) sit 14th, two wins outside the finals places.
For the Saints, Nasiah Wanganeen-Milera (28 disposals) and Jack Sinclair (31 touches) were classy, while Rowan Marshall (24 hitouts, seven clearances) and Jack Steele (20 touches, six clearances) got to work on the inside.
Sam Collins worked hard in defence all game for the Suns, while Sam Flanders (42 disposals) continued his prolific form off half-back and Noah Anderson (29 touches) fought hard.
St Kilda's Dan Butler kicked two goals in the opening term and three for the game.
Butler's first came in controversial fashion after Andrew was penalised for shoving him off the ball, with the small forward going down easily then converting.
It helped the Saints to a 12-point lead at the first change.
But St Kilda suffered an early blow, with defender Dougal Howard forced off with a hamstring injury and replaced by veteran Seb Ross.
Across the second and third quarters, the Saints failed to make their dominance count and led by just eight points at the final change.
Talented young Suns defender Bodhi Uwland took a terrific flying contested mark over Max King early in the final term, then stopped a would-be goal with a fingertip smother.
The Suns kept pressing and finally hit the front for the first time when Miller swooped on a Ned Moyle tap-down and snapped truly.
But King's late goal left the Suns to rue what might have been.
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