Lewis and Miyazato each shot a 6-under 65 on Friday at the Bay Course at the Stockton Seaview Hotel and Golf Club.
Paula Creamer and Mariajo Uribe are tied for third at 4 under. Maude-Aimee Leblanc of Sherbrooke, Que., is at 3 under, while seven players are another shot back, including Lexi Thompson and Christina Kim.
Yani Tseng shot an even-par 71 while defending champion Brittany Lincicome finished with a 72.
The morning half of the field had the better of the weather, as skies darkened and the winds picked up around mid-day.
Uribe was the only one of the leaders with an afternoon tee time.
Miyazato, who is seeking her first LPGA title, played in the first group and got off to a fast start. She birdied Nos. 3 and 5, then took advantage of the wind to reach the par-5 ninth in two. She drained a 20-foot eagle putt with a left-to-right break to make the turn in 3 under.
"The second shot I think was 220," Miyazato said. "I hit a seven-wood. I thought it was more short than on the green."
She birdied two par 3s on the back, Nos. 11 and 17.
Lewis, who won her second LPGA title in Mobile in April, was in the middle of her round when the conditions started to change. Playing the back nine first, she made the turn in 2 under before starting her second nine with a birdie, a double bogey and an eagle.
"The first nine holes were pretty nice," Lewis said. "There wasn't much wind. And then, I guess we were making the turn onto one, and the wind just came out of nowhere.
"So it got a little crazy on the back nine but I played really well."
Lewis reached the green at the par-5 ninth in two but missed a seven-foot eagle putt that would have given her the outright lead. But she said she's been playing with a lot of confidence over the last 14 months since claiming her first career win at the 2011 Kraft Nabisco Championship.
"And it's all confidence," she said. "If I'm comfortable over a shot and I feel good about it I'm probably going to hit a good shot. And so good shots breed more confidence."
Creamer, who tied for second in this tournament as an amateur in 2004, reached No. 18 in two and drained her eagle putt.
Creamer started her round just a few minutes ahead of Lewis and also felt the impact of the wind.
"The golf course definitely played hard today," she said. "It was very windy.
"The harder holes on the golf course were even more hard. There were a lot of long clubs into par 4s where we're normally hitting six or seven irons that now we're hitting woods into."
NOTES: A total of 23 players broke par. ... This tournament was first contested in 1986. It disappeared from the schedule after 2006 before returning last year. ... Morgan Pressel, back in action after her controversial loss to Munoz in the semifinals of the Sybase Match Play Championship, shot a 74.