The world No 1 shot a course record 62 to be 12 under for the tournament and three clear at the halfway point.
The New Zealander birdied four of the first six holes and had seven birdies and a bogey on the back nine to get to 12-under 132 in the season finale.
Ryann O'Toole (67) and So Yeon Ryu (68) were tied for second, while Sei Young Kim (68) and Beatriz Recari (68) followed at 8 under.
Ko spent a late night on the range with her coach after the first round tweaking things.
"Going into today I just wanted to focus on my game and I knew I had a great pairing.... and maybe it was the great vibes I got from them but obviously it's a great round and I'm in a better position than I ever could have imagined," she said.
"Over the weekend I just have to focus on me."
