Seeking her sixth LPGA Tour victory, 20-year-old Canadian Henderson opened with bogey-free rounds of 68 and 66.
"I feel like I'm in a great spot obviously at the top", said Henderson, who has held the 36-hole lead during four of her five career LPGA wins, including at the 2016 KPMG Women's PGA Championship.
With bogeys on holes two, nine and 12, Ko wasn't making headway, but she picked up her game late, adding to her birdie on hole three with three successive ones from 14 to 16, before also going under on 18.
Pernilla Lindberg and Inbee Park were back together again on the leaderboard at 6 under, two weeks after Lindberg beat Park on the eighth extra hole in the major ANA Inspiration. That stretched to five at the turn Friday, before putting problems brought the field back into it.
Henderson doubled her overnight advantage to two strokes with birdies at the third and ninth, before bogeying the par-three 12th and missing a short birdie chance at the next.
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Also still in with a shout are the likes of Lizette Salas and World No 1 Shanshan Feng, who both lie just three strokes back after rounds of 71 and 70 respectively. "I missed a couple putts, which you could argue that mentally I wasn't there because of a couple mishits, but I think to recover from that and kind of put it in the past and then go out and make some more birdies".
Munoz, who has struggled with illness injury the past few years, climbed 13 places the final day. She parred her final 11 holes.
Henderson and fellow Canadians Alena Sharp, Anne-Catherine Tanguay, Brittany Marchand and Maude-Aimee Leblanc wore green and gold ribbons in memory of those killed in the Saskatchewan bus crash involving the Humboldt Broncos junior hockey team.
Hawaii native Michelle Wie shot a 73 and is tied for 31st.
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