The American made a clutch birdie on No. 17 to take a two-stroke lead to the final hole at the Accordia Golf Narashino Country Club.
The American, who has roots in Japan, was steady throughout and came up big on the final hole.
The former world No. 1 amateur is alone in fifth place after a spectacular 63 at the Accordia Golf Narashino Country Club.
The defending champion will need a strong round to get back into contention as he bids to become the first two-time winner of the tournament.
The Kobe native finished two shots off the pace after entering the final round in a three-way tie for the tournament lead in Portland, Oregon.
The 19-year-old became the youngest winner of the JLPGA Championship Konica Minolta Cup, earning the title with an 8-under 64 in the final round.
“I hope I have created a pathway for not only Japanese players but all Asia-Pacific players to pursue the dream they have,” Nakajima said.
“It’s just amazing. I just can’t believe it,” said the 17-year-old Baba, who captured the title by the largest margin since 1961.
“I am both frustrated and happy to get a result like this on this difficult and wonderful course," said the golfer known as "Smiling Cinderella."
The 22-year-old Kobe native captured her first LPGA Tour title with a career-best round in a come-from-behind victory.
Fittingly, the Argentine legend scored the first goal in the French club's tour-opening win over Kawasaki Frontale.
"I would like to take a leap forward with my experience of winning this time," Agu said after securing Japan’s first-ever stage victory on the tour.