The 27-year-old Oklahoman had five birdies and sealed her second LPGA Tour title by two-putting for par from 20 feet on No. 18 to finish at 14-under 202.
Lee, who had to finish four of her second-round holes in the morning because of a rain delay Friday, closed with a bogey-free 68.
Prammanasudh, (pronounced PRAH-mahna-sood), was sharp and steady all day, never allowing anyone to catch her.
"With the way the talent is on tour, you can't really let your mind slack at all," she said. "What I was really focused on was just being really in the moment, focusing on each one of my targets and just keeping my mind focused on what I needed to do."
The former University of Tulsa star also won the Franklin American Mortgage Championship in 2005, the last tournament she led heading into the final round before this week.
Prammanasudh said this win, worth $180,000, was much sweeter.
"The first kind of came up on me by surprise. I wasn't expecting to win so early," she said. "Then you know you put in a lot of hard work to try to get that second one. I'm definitely glad I played well enough to come out on top."
After holing her final putt, a 2-footer for par, she shook her arms in the air and kissed her husband, Pete Upton, who also is her caddie.
Rookie Angela Park (71), making her second LPGA Tour start as a pro, Japanese star Ai Miyazato (66) and 18-year-old Morgan Pressel (69) tied for third at 11 under.
Park and Pressel, who finished fourth at the season-opening SBS Open, are both 18 and were vying to supplant Paula Creamer as the youngest winner of a full LPGA Tour event.
With a three-hour rain delay Friday, 70 players had to return to the course Saturday morning to complete the second round. Prammanasudh was not affected by the delay and had more than 24 hours to relax and prepare.
"Ironically, it was the exact same situation for my first win," she said.
Prammanasudh took sole possession of the lead early, sinking short birdie putts on the first two holes to take a two-shot lead. She missed the green and bogeyed the par-4 third, but hit an aggressive second shot over the water on the par-5 fifth that set up a two-putt birdie from 30 feet to get back to 12 under.
Park and the big-hitting Lee also birdied the hole to stay a stroke behind Prammanasudh.
"There were a lot of chances for me to make more birdies but I just couldn't do it," said Lee, who won the 2005 CJ Nine Bridges Classic in South Korea to become the 14th non-LPGA member to win an LPGA event.
Prammanasudh parred the next five holes before holing a 5-foot birdie putt on the par-4 11th hole.
After hitting a 3-wood to reach the green in two, Prammanasudh missed a long eagle putt, but tapped in for birdie with her belly putter on the par-5 13th to reach 14 under. Lee stayed a stroke behind with a birdie.
Lee's best chance to tie Prammanasudh was on No. 17, but she missed an 7-foot downhill birdie putt. Lee had a slim opportunity to force a playoff, but missed a 50-foot birdie putt on 18.
The 21-year-old Lee said Prammanasudh was consistent off the tees and on the greens, making her difficult to catch.
Park was tied with Prammanasudh for the lead heading into the final round at 10 under after playing nine of her second-round holes earlier in the day. But she couldn't make a move, missing several birdie attempts.
She sailed her tee shot into the bunker on the par-3 12th for bogey that dropped her three shots off the pace. Park earned $64,288.
Miyazato's third-place tie matches her best finish since joining the tour last yearShe also tied for third in the 2006 LPGA Championship.
Miyazato, one of the smallest players in the field, had the largest gallery with dozens of reporters and photographers from her native Japan following her every move.
She had a bogey-free round with six birdies.
Cristie Kerr, assessed a two-stroke penalty in the opening round, closed with a 65 to tie for sixth with Vicki Goetze-Ackerman at 10 under. Mi Hyun Kim (69) was another stroke back along with Wendy Doolan (70).
Creamer (67), who won the SBS last week for her third LPGA Tour title, was 7 under along with Aram Cho (70), Michele Redman (70) and Nicole Castrale (71).
Karrie Webb (71) and Se Ri Pak (70) were among the group at 6 under.