The South Korean shot a final round five-under 66 to finish at 18-under.
The US$1.1 million winner's prize, down from US$1.5 million last year, is the richest in women's golf.
"I still can't believe it, that I'm here, that I won this tournament," Jin Young Ko said.
Compatriot Sei Young Kim held a one-shot lead at the start of the day and was in position to defend her title in the CME Group Tour Championship, take player of the year honours, win the money title and possibly even move to No. 1 in the world.
But she slipped back to finish five shots back from Jin Young Ko in a share of second missing out on the money but still claimed Rolex Player of the Year honours.
Danielle Kang won the Vare Trophy for the lowest scoring average.
The win wrapped up a wire-to-wire year in the No. 1 spot for Jin Young Ko, who has held the ranking since July 29, 2019. She moved to US$5,600,824 in career earnings, making her the 71st player in LPGA history to cross the US$5 million mark.
Jin Young Ko played only four LPGA events in 2020 — she competed six times on the Korean LPGA while riding out the coronavirus pandemic at home — but Sunday's win and a check for US$487,286 for finishing second in last week's U.S. Women's Open helped push her season earnings to US$1,667,925. That would have been good for fifth-best on tour last season, when each of the 21 leading money-winners all appeared in at least 20 events.
Today marked the end to the 18-event LPGA season that was cut almost in half by the pandemic and was shut down for 5 1/2 months from mid-February through the end of July. Next season is scheduled for 34 events, starting with the Diamond Resorts Tournament of Champions in Lake Buena Vista, Florida, from Jan. 21-24.
- With AP