Ko birdied the final hole for her third LPGA Tour victory and first as a professional, holding off Stacy Lewis and Jenny Shin, the Associated Press reported.
The teen made a two-metre putt moments before Lewis knocked in a putt of her own to finish one stroke back.
"The 18th hole I knew how loud the claps were and that I needed to get close and give myself a birdie chance," Ko was quoted as saying afterwards.
After beginning the day a stroke behind Lewis, Ko birdied three of her final four holes on the front nine on the way to a 3-under 69 and 12-under 276 total at Lake Merced.
Ko earned $US270,000 for the win and will move up two spots to No 2 in the next world ranking.