Ko was tied for the lead coming into the 54th and final hole at the rain-shortened Evian Championship, but she couldn't execute on the tricky par four, bogeying the last and dropping back to finish in a share of third at eight-under par for the tournament.
Sweden's Anna Nordqvist won her second major in a playoff, beating American Brittany Altomare after both players carded fantastic final rounds of 66 to leap up 10 spots into contention.
Ko finished one shot back, with her third placing her best finish in a major in her last six attempts, and marking her eighth finish of third-or-better in a major championship.
In the end, it was hard for anyone to match the stellar rounds of Altomare and Nordvist, who stormed up the leaderboard. As they made their rise, most of the overnight leaders fell away, with Ko one of the few exceptions.
Coming into the final round three shots adrift, birdies on holes three and four kept Ko in touch with the leaders early on, though a bogey on the par five seventh diminshed her chances.
Par fives were proving to be a problem for Ko's comparatively short driving game off the tee, and a bogey on the 13th - also a par five - looked to have ended her chances of contention.
At that point, Ko was at six-under, four shots back of leader Moriya Jutanugarn, but she slowly gained back that ground.
A birdie at 14 immediately offset her prior bogey, before Ko suddenly reversed her previous par five performance. A stunning chip-in on the 15th, flopping a shot from the rough and running it into the cup, launched her back into the picture.
All of a sudden, Ko was at nine-under, and a bogey from Jutanugarn saw four players tied for the lead with just three holes to play.
As rain began to spit and the winds continued to escalate, Ko managed to navigate safely through her next two holes, overcoming a less than ideal approach shot on 17 to smartly two-putt from distance.
A similar recovery was not possible on the par four 18th however. A slightly off-centre drive left Ko in the first cut of rough on the right, needing to clear a sizeable pond to make the green.
Not content with settling for a playoff, Ko grabbed the fairway wood, and while she avoided the water hazard, her approach landed in the rough to the left of the green.
Needing to get up and down, Ko's putter deserted her at the wrong moment, leaving the 20-year-old to complete a two-under 69, and missing out on the playoff.
Her fate was matched by Jutanugarn, who similarly bogied the last to miss the playoff, which was eventually, and somewhat farcically, won by Nordqvist on the first playoff hole as rain and hail fell.
Nordqvist's win makes it nine consecutive different major winners since Ko went back-to-back, pinpointing the increased competition level in women's golf.
Despite the ending, Ko's performance makes it two consecutive strong weeks, following her second place in Indianapolis the week prior.
The former world number one will be a good chance to continue that strong form when she tees up at the New Zealand Women's Open, starting on September 28 at Auckland's Windross Farm Golf Course.
