The South Korean, 24, who earned her first major success at the ANA Inspiration in April, shot a final-round 67 at a wet Evian-les-Bains to finish on 15 under par.
American Jennifer Kupcho carded a five-under-par 66 - the lowest round of the day in tricky conditions - for a share of second place alongside Kim Hyo-joo and China’s Shanshan Feng.
Overnight leader Kim finished with a two-over 73 on Sunday as her chances faded.
World number one Park Sung-hyun, who went into the final round in France just a shot off the pace, finished five shots adrift of Ko after an error-strewn 75.