Miyazato, who won her first LPGA title at the Evian Masters two years ago, made five birdies for a 13-under total of 203. She heads into Sunday's fourth round ahead of a group of four players, including Kraft Nabisco winner Stacy Lewis.
"I hit the ball really well today, and my putting was really good as well," the 26-year-old Miyazato said. "I was really calm out there, so that's why I didn't have a bogey."
With the course lending itself to aggressive golf and the pins made for attacking, Miyazato is expecting to come under heavy pressure on Sunday as she bids for her first title of the year, and her second Evian Masters trophy in three years.
She was sixth at the recent U.S. Open, but her best result this year was a tie for fifth at the Sybase Match Play Championship in May.
"Two shots leading is still nothing on this golf course, I think. Still so many players can shoot low score tomorrow," Miyazato said. "It's still wet on the fairway, but the greens are really receptive, you can still be aggressive."
I.K. Kim of South Korea moved into contention after shooting up the leaderboard with a brilliant round of 64 to sit three shots behind. Kim made six birdies on the first eight holes and had nine overall.
"I had a great round, I have to say. Everything was clicking," Kim said. "Once you get a good feeling out there it kind of builds up, you get a snowball (effect). I'm excited to see myself on the leaderboard going into tomorrow."
Kim's score would have been even more impressive if not for a bogey on the fifth hole, although she hit three straight birdies after that.
"I was on the fairway and just pulled it left," she said. "It could have been much better if I hit it five feet right ... I hope I can birdie (it) tomorrow."
Kim is looking for her first tournament win this year after third-place finishes at the Kia Classic and the LPGA Thailand — where she hit a round of 63, her best of the year.
Hong matched Miyazato's round, Stanford and Lewis had 69s and Saiki finished with a 70.
Lewis also expects to see some very low scores on Sunday.
"The course is so soft and so scoreable you know somebody's going to shoot 5 or 6 under," she said. "You just hope that it's you. You have to make birdies, go for some flags and try to make some shots that you normally wouldn't."
Lewis, however, felt she could have put herself in a far better position to challenge Miyazato.
"I'm a little bit frustrated with the way I played today," she said. "I hit a ton of good golf shots and just had, I mean, probably four or five putts lip out."
Defending champion Jiyai Shin of South Korea was undone by two early bogeys and is five shots back from Miyazato at 8 under, along with Sweden's Caroline Hedwall.
Despite the improved weather conditions, former U.S. Open champion Paula Creamer had a disappointing round under the sunshine with four bogeys and only made level par to stay 7 under.
Stanford, meanwhile, hopes to clinch her first title since February 2009, when she won the SBS Open at Turtle Bay.
The 33-year-old came quite close at this year's U.S. Open, finishing fourth, and at the Kraft Nabisco, taking third.
"I've always been a big believer in you learn how to win. If you can get into that position more and more, it's just more learning experience," Stanford said. "I'm excited to have an opportunity to be in the hunt here. Never really had an opportunity to win here."