Yubol, who was penalised one shot in the second round on Saturday for going over her maximum time, birdied the last two holes for a 66 - just shy of Boutier's nine-under winning total for the 54-hole tournament.
Soo Bin Joo, the 22-year-old South Korean going for her first LPGA Tour title, lost her overnight four-shot lead at the turn as she stumbled to a 73 and share of fourth place.
Boutier finished the front nine with two straight birdies to reach 7 under, and that gave her a share of the lead when Joo made bogey on the par-4 eighth.
Boutier then hit her approach to 4 feet for birdie on 10th. Joo caught her with a birdie on the ninth but couldn't keep up the rest of the way.
Cassie Porter was the leading Australian, wrapping up a good week with a closing 67 to tie for ninth at four under. Robyn Choi (72) was tied 51st, with Steph Kyriacou (73) tied 58th and Gabriela Ruffels (76) tied 68th.
Boutier also won the tournament in 2021.
"To have a chance to win today is definitely something very special," said 32-year-old Boutier. "I think it's great tournament, very special for me, so really excited to be able to have another win here."
Boutier now has seven career LPGA title and 12 worldwide. She had struggled to start this year, with a tie for ninth her best finish among 10 tournaments.
"I feel like my game has turned around the last few weeks," she said. "I could see it coming together, and I definitely did not expect it to come together this week and today."
Yubol notched her second runner-up finish of the year, having finished four shots behind Nelly Korda in Mexico.
Ireland's Lauren Walsh (67) finished third at seven under.
Joo took her tough last day philosophically.
"It was so fun. It was my first time leading the tournament, and I think I did my best out there as much as I can and I prepared well and I'm very proud of myself," Joo said. "I was trying to do my best to stay mentally calm, and I think I still got to work on that a little more."
The ShopRite LPGA is one of two 54-hole events on the schedule, and the field was particularly weak this year — one player from the top 10 — because of timing. The U.S. Women's Open is next week across the country in Los Angeles, held at Riviera for the first time.
