Lee carded a final round two-under par 70 for a tournament total of 13-under, one better than American Jessica Korda (71)and two-strokes ahead of world number two Ariya Jutanugarn (70).
After the Australian made her only bogey on the 17th, Ariya drew level with one hole to play but the Thai bogeyed the last to settle for a third-placed finish and Lee sank a birdie putt to pip Korda.
"I think my heart was coming out of my chest," Lee said. "Actually even on that last putt. I was a little nervous all day, actually. I had to really work for this win. I'm glad I came out on top. They're great competitors."
Lee won the LPGA's Kingsmill Championship in May last year and the Lotte Championship in Hawaii in April.
(Reporting by Ian Rodricks in Bengaluru)
