The 22-year-old, who started the day with a three-shot cushion, opened with a bogey as she carded a 74 - her over-par round of the week - at Champions Golf Club in Houston.
That three-over effort on the Cypress Creek Course left her sitting on four-under, just ahead of American Amy Olson (71).
Shibuno, who dropped shots at both the 14th and 18th, said the nerves of being in the final group played a factor in her Saturday struggles, as well as the feeling of not having fans outside the ropes.
“Last year when I won the major (at Woburn), there was a large number of people out in front of me and because of the audience, that gave me power and also it's easy for me to get on a momentum as well,” said Shibuno, golf’s ‘Smiling Cinderella’.
“However, now there's no people, no audience and it's very difficult for me to get on a momentum, because when I get a run of birdies, when I get the birdie, it's silence.”
Olson, who led after an opening 67 that included a hole-in-one, nearly holed out from the fairway with an 8-iron at the 17th as she earned a place in the final group.
“I'm really pleased with how I played today. It was such a grind,” said Olson, who played in the final group at the 2018 ANA Inspiration and 2018 Evian Championship but came up short on both occasions. “Pars were a great score on every single hole today.”
Thailand’s Moriya Jutanugarn (72) and Korean Ji Yeong Kim2 (67) are joint-third on one-under, with former Kiwi Lydia Ko (72) lurking in a group on level-par.
Playing alongside Shibuno in Saturday’s final group, amateurs Linn Grant and Kaitlyn Papp shot seven-over and four-over respectively to drop down the leaderboard.
Today’s fourth-round tee times have been moved to 7:45 am CST due to anticipated inclement weather.
Play will still begin on the first and 10th tees of the Cypress Creek Course.