The South Korean shot a 5-under 67 to finish at 16-under 272 at the tricky Locust Hill course. A 22-year-old in her second year on the tour, Ji had a previous best finish of second to Pettersen at South Koreas Kolon Championship in October.
Pettersen shot a 72 and surrendered a three-stroke lead on the sunny, 75-degree day. Ji got in front for the first time with a 7-foot birdie putt on No. 15, where Pettersen missed a 5-footer for par.
The 28-year-old Norwegian has finishes of second, third and ninth this year. She won five times on the tour in 2007.
Jeong Jang (69), who won in Rochester in 2006, tied for third at 12 under with fellow South Korean Hee-Won Han (69).
Cristie Kerr (69), preparing for her title defense in this weeks U.S. Womens Open, took fifth place at 11 under, two ahead of top-ranked Lorena Ochoa (69), Christina Kim (68), Japans Ai Miyazato (72) and South Korean Inbee Park (74).
Ochoa, a six-time winner this year, won in Rochester in 2005 and 2007. With $2 million in season earnings, she extended her lead on Annika Sorenstam (69) to more than a half-million dollars. The Swede, who ended at 2 under in a tie for 33rd, is stepping away from the tour at the end of the season.
Michelle Wie closed with a 68 to finish tied for 24th at 4 under.
Ji already had ties for fourth and ninth this year. She earned $300,000 in the $2 million tournament to surge from 42nd to 10th on the money list with $471,413.
Pettersens three-shot lead dissolved over the first three holes. Ji opened with a 12-foot birdie putt and Pettersen bogeyed No. 2, her approach shot obstructed by a tree. Ji deftly chipped in from the back fringe on No. 3 to draw level.
Pettersens chip to 3 feet from thick rough in front of the par-5 eighth got her two ahead again. She restored her three-stroke cushion when she sank a 10-foot birdie putt on No. 11 and Ji missed from 5 feet on the next hole.
The momentum swung back when Ji made a 20-foot birdie on No. 13 and Pettersen drove into the left rough and failed to get up and down from a greenside bunker. After Ji moved into the lead at No. 15, both players birdied the par-5 17th. Ji extended her lead to two with a tap-in on the final green after Pettersen missed from 5 feet for par.