Ko, the world's top amateur, broke Japananse star Ryo Ishikawa's mark of 15 years, 8 months, and Australian Amy Yang's women's record of 16 years, 192 days in the Australian Ladies Masters.
The South Korean-born New Zealander shot a 3-under par final round of 69 to finish 14-under for the tournament, four strokes clear of Becky Morgan of Wales in the 54-hole tournament at Oatlands Golf Club.
Britain's Laura Davies closed with a 71 and a 54-hole total of 216, 14 strokes behind.
"To be part of history is like a miracle," Ko said. "It's not something you can have by clicking your fingers."
"My driver and iron play were probably the nicest to me over the past two days," Ko added. "I also putted well, but I was in good position on most of the greens because I was able to make approaches from good places on the fairways."
Ko, a Grade 11 student at North Harbour near Auckland, plans to play about 30 tournaments this year, including professional events over the next two weeks at the Australian Masters at Royal Pines on the Gold Coast and the LPGA's Australian Open at Royal Melbourne.
"I'll play in mostly amateur tournaments after that, and my schedule looks pretty busy for the next several months," Ko said.
Ko, who says her role models are American golfers Michelle Wie and Alexis Thompson, moved to New Zealand with her family from Seoul in 2003.
"My sister (Sura) was attending school in Canada, and we were going to move there, but when I started playing golf regularly, we decided New Zealand would be the best place to come because of the weather," she said.
Her mother, Tina, travels with her to tournaments and her father, Jil-hong, is a banker based in Auckland.