The 23-year-old, who won the Women’s Australian Open in February, recorded three birdies and two bogeys for a 54-hole total of 10-under at Lake Merced Golf Club.
South African Lee-Anne Pace and South Korean Choi Na-yeon were at seven-under after scores of 69 and 71.
LPGA officials met with Nomura and her caddie after her round to discuss a possible rules violation on the sixth where she had an awkward side-hill stance in a greenside bunker with the ball below her feet and had to dig in her left foot.
Rule 13-3 states: “a player is entitled to place her feet firmly in taking a stance, but she must not build a stance,” but the LPGA rules committee later said in a statement “it was determined that no breach occurred”.
An infraction would have cost her a two-stroke penalty.
“For me the two-stroke penalty, it wouldn’t really have made a big difference,” Nomura told reporters.
“If I did something wrong, I have to accept it. But there was really no clear rule about what the guidelines were, so I would just focus on my game and just leave it at that.”
Nomura began the round with a three-shot advantage and increased that lead when she rolled in an 18-foot birdie putt at 10. But she dropped a shot with a bogey at 12 and closed with six straight pars.
Canadian Brooke Henderson (69), Scot Catriona Matthew (71), American Gerina Piller (72) and South Korean Ryu So-yeon (73) are tied for fourth at five-under.
Two-time defending champion and world number one Lydia Ko carded a 73 for a four-under total.
Original source: Nomura skirts violation to hold lead