Ko, who entered the final round with a one-shot lead, ended with a three-stroke victory at 13-under 275.
The Korean-New Zealander became the first amateur to win an LPGA event since JoAnne Carner in 1969.
She added the honor to another she claimed in January when, at age 14, she became the youngest player to win a professional event -- claiming the Women's NSW Open.
Ko also won the U.S. Women's Amateur Championship two weeks ago.
Finishing a distant second at the Canadian Women's Open was Evian Masters winner Inbee Park (3-under 69) at minus-10.