A field of 72 played the first 36 holes at nearby Champions Retreat before the event moved to the famed Masters layout, with everyone having a practice round Friday but only the top 30 advancing to compete in the last 18 holes of the tournament.
Kupcho was even through 12 holes before coming on in a big way down the stretch, playing her last six holes in 5 under.
History dictates the Masters does not begin until the back nine on Sunday and that held true for the women who played their final round on Saturday, as Kupcho, the world's top ranked amateur, exited Amen Corner erasing Fassi's two shot lead with a brilliant eagle on the par five 13th.
Fassi answered with a 10-foot birdie putt to regain the lead, and Kupcho made a decision to aim her 3-hybrid to the bunker right of the green on the par-5 15th.
Mehaffey carded four birdies and four bogeys in her second round and is six shots behind American Jennifer Kupcho.
After bogeying the first hole, Fassi had four birdies on the front nine.
American duo Zoe Campos (72) and Kaitlyn Papp (74) shared fifth place on one under.
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"You are now part of history of Augusta National along with all the great Masters champions who have been right here in this Butler Cabin", Augusta National chairman Fred Ridley said as he presented Kupcho with her trophy in the same location where the Masters champion is presented with the winner's green jacket.
Ridley announced a year ago the creation of the Augusta National Women's Amateur to provide a spark for women's golf. Sorenstam and her daughter walked with the final group.
The University of Arkansas and Blessings Golf Club are the proud hosts of the 2019 NCAA Women's and Men's National Championships.
Kupcho's elation was mixed with relief as she struggled with a migraine and blurred vision from the eighth through 11th holes that threatened to scuttle her title hopes.
"We both are good friends, so I think it will be a lot of fun, and we're both good at golf - really good at golf", she said. She was five shots behind toward the end of the round when she used her power to set up easy birdies on the reachable par-4 seventh and the par-5 ninth.
"I think my hands were shaking on my first tee shot, but the course is awesome.as I think we all know" Caterina Don said.
"I think it's going to have a great effect around the world".