Ko held her nerve with a final-round two-under-par 70 on Sunday to finish two shots clear of Ireland’s Leona Maguire (72).
The victory clinched Player of the Year honours for Ko and also the biggest cheque in women’s golf history.
Ko’s $US2 million ($A3m) pay day took her season earnings to $US4,364,403 ($A6.6m), leaving the New Zealander to also win the season-long money list.
Lee finished second in both the Player of the Year and money race in 2022 after fading to a tie for 33rd in Naples with a closing with a five-over 77.
Australia’s World No.5 bogeyed six of her last 10 holes in her worst finish of a sapping season.
Lee had the chance to be crowned player of the year if she finished in the top-10 and above Ko in the last event of the LPGA season.
Instead, the 26-year-old ended the tournament 16 shots behind Ko, who also claimed the Vare Trophy for best scoring average for the second consecutive season and second time in her career.
Lee, though, still ended her own stellar season with the Annika Major Award for major player of the year following her commanding U.S. Women’s Open triumph in June and also pocketed a cheque for $US1 million ($A1.5m) as the AON Risk Reward Challenge winner.
But the Sunday spoils were all for Ko, who choked up after holing out at the last to claim her first player-of-the-year award since 2015.
“There was a lot of things on the line today,” Ko said.
“I really wanted to play the best golf I can. I knew it would be a tough battle, especially with how tough the conditions were.”
With three victories, plus nine additional top-5s in 2022, the former teenage prodigy also posted her first multiple-win season since 2016 to edge ever closer to a seemingly inevitable place in the LPGA Hall of Fame.
Ko would also have regained the top ranking if World No.1 Nelly Korda finished outside the top-20.
But the American tied for 10th at eight-under after closing with a 70.
Still, Ko headed for the off-season with plans to get married feeling blissfully content as World No.2.
“This is my last tournament as a single lady,” she said with a laugh at the trophy presentation.
Hannah Green, the only other Australian in the elite 60-player field for the season finale, tied for 33rd with Lee at one-under following a final-round 71.
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