Ko - like Day a former world No.1 - birdied the 17th hole and had a tap-in par at 18 as the pair edged out Canada's Brooke Henderson and Corey Conners by one shot.
Ko and Day posted their second straight round of six-under-par 66 to finish at 26-under 190 for the three-day event.
The tournament featured 16 mixed teams with one male and one female player.
The teams played a scramble format on Friday and foursomes (alternate shot) Saturday.
Sunday's final round was a modified four-ball, in which both teammates teed off, then switched balls for their second shots and played that ball the rest of the hole.
Ko and Day had a two-stroke lead entering the final round and combined to card six birdies without a bogey on Sunday.
"It felt like the most stress-free win because I just knew (Ko) was going to step up in the end, which was fantastic," Day said.
"It was a fun week. Having the two tours join this week was a fun way to finish the year out."
Ko also enjoyed the format of the season-ending mixed-gender tournament.
"I learned a lot, whether it was short-sided chips or just how to commit and hit bombs down there," she said.
"This has just been a great start for the two tours coming together and having a mixed event.
"I really hope this is something that continues for a long time."
Conners and Henderson had a wild start. They were able to card an eagle on the par-5 first hole and birdied the par-4 second before having to settle for a double bogey at the par-4 third.
They added a second eagle when Conners holed out at the par-4 ninth, and they birdied five of the next six holes to get to 25 under overall and put the pressure on Ko and Day with a final-round 63.
Swedes Madelene Sagstrom and Ludvig Aberg were third at 24 under after a final-round 60, with 10 birdies and a late eagle.
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