World No.4 Yamashita, the 2025 Women's British Open champion, shot a six-under 66 on Friday to take a two-stroke at 13-under 131 on the Kuala Lumpur Golf and Country Club course.
Spain's Julia Lopez Ramirez birdied three of her final four holes for a 66 and was tied for second with France's Pauline Roussin-Bouchard (69), who had led by a stroke after the first round.
A Lim Kim had a 64 and was in fourth place, three strokes behind Yamashita.
Choi followed her opening 67 with a round of 69 to be five shots behind Yamashita and tied ninth as she continues to seek a maiden LPGA Tour win, having joined the tour in 2019.
Davidson climbed with a 67 to be just a shot further back.
Of the other Australians, Cassie Porter battled to a 73 and was tied 39th at two under, with Grace Kim (70) at one under, followed by Hannah Green (71) at one over.
English star Charley Hull had five birdies in her first six holes for bogeyed two of her final three holes for a 69 and was tied for fifth, four strokes behind.
Haeran Ryu, a major winner this year at the Women's PGA Championship and at the Evian Championship, withdrew before her first-round tee time due to a strained finger ligament. She was the highest-ranked player in the tournament in the absence of No.1 Nelly Korda and No.2 Jeeno Thitikul.
Last week, Yuri Yoshida won the BMW Ladies Championship in South Korea, the fourth Japanese player this season to win on the LPGA Tour, joining Yamashita, Shiho Kuwaki and Yuna Nishimura. Yoshida shot 70 Friday and was at 5-under.
Next week, the LPGA's four-week, late-season Asian swing ends with the Toto Japan Classic at Omitama outside Tokyo.
with AAP
