Rookie Jang Ha-na of South Korea posted a 69 for 272 to share second place with American Gerina Piller, who fired a 67.
World number one Ko was in a tight battle to hold on to her edge in the jackpot race, with South Korean Park missing a birdie putt at the 17th as did Thompson that would have put them out in front for that prize.
World number two Park shot a 69 for 276 and sixth place in the tournament to finish second in the race, while American Thompson returned a 68 for fourth place on 274.
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"I think the hole is smaller than the ball today," said Ko, who carded a final-round 72 for 11-under 277 and a tie for seventh.
Ko's par putt at the last lipped out and she did not learn she had won the jackpot until after she walked off the green and had a quiet, emotional moment.
"I'm happy that the season is over and I can relax now," said Ko, last year's Rookie of the Year.
"It was kind of a tough day. I tried to stay patient all day. Every emotion went through me."
Ko also secured Player of the Year honours, while Park narrowly edged her out for the Vare Trophy for the season's lowest scoring average.
"Earlier in the week I said if I could choose one of the awards, I would love to be the Player of the Year," said Ko. "To know that I am the Player of the Year, it's an awesome feeling."
Ko became only the fourth LPGA player to follow up rookie honours with being Player of the Year, following Nancy Lopez, Beth Daniel and Annika Sorenstam.
The 28-year-old Park, who won two majors this season, also celebrated another achievement.
By winning the Vare Trophy, Park earned her 27th point to qualify for the LPGA Hall of Fame, where she will be enshrined after completing a 10th LPGA season.
"Coming to today, I knew that I needed one point to wrap up the season. Not to think about a million dollars or the Player of the Year or the Vare Trophy. My focus was really getting the 27 points," said Park.
(Reporting by Larry Fine in New York; Editing by Ken Ferris/Greg Stutchbury)
