The 15-year-old South Korea-born New Zealander finished with a five-under-par 67 to win by three shots.
She broke the age record of 16, set by Lexi Thompson in the Navistar LPGA Classic in Alabama last September.
Only four other amateurs have ever won on the Tour, and Ko became the first since JoAnne Carner took the 1969 Burdine's Invitational tournament.
In January, Ko won the New South Wales Open in Australia at 14 to become the youngest player to win a professional tour event, a mark broken by 14-year-old Brooke Henderson in June in a Canadian Women's Tour event in Quebec.
Ko also won the US Women's Amateur two weeks ago in Cleveland, Ohio.
Starting the final round at The Vancouver Golf Club one shot clear, she surged away from the field on the backward nine, shooting five birdies in six holes to finish at 13 under.
Inbee Park shot a 69 to finish second on 10 under, while US Women's Open champion Na Yeon Choi, Chella Choi and Jiyai Shin tied for third at eight under.

In a speech he said that he expected rates to rise over the next three years, reaching "about half as high as historical averages", or about 2%.
But he added that shocks to the economy could change the timing and the size of any rate rise.
Interest rates have been at 0.5% for six years as the UK economy recovers from the financial crisis.
The Monetary Policy Committee will "have to feel its way as it goes," Mr Carney said in a speech at Lincoln Cathedral.
He added: "Short term interest rates have averaged around 4.5% since around the Bank's inception three centuries ago.
"It would not seem unreasonable to me to expect that once normalisation begins, interest rate increases would proceed slowly and rise to a level in the medium term that is perhaps about half as high as historic averages.
"In my view, the decision as to when to start such a process of adjustment will likely come into sharper relief around the turn of this year," he added.
His comments come a day after unemployment rose for the first time in two years.
"That suggests the Bank's interpretation of those statistics is that unemployment falls are now being held back by skills shortages," said the BBC's economics editor Robert Peston.
"And those skills shortages are also responsible for rising wage inflation."
On Tuesday, outgoing MPC member David Miles, regarded as someone who is cautious about the impact of rise, surprised markets by saying it was "likely to be right" to hike rates soon.
On Wednesday, Janet Yellen, the chair of the US's Federal Reserve indicated that interest rates are likely to rise in the US this year. That could be a few months earlier than in the UK if indeed the Bank of England were to move in the new year.
If rates were to rise early in the new year, from the current all-time record low of 0.5%, that would be three or four months after the expected equivalent move by the US Federal Reserve.
Now for those of you with big debts looking for reassurance that you are not going to be financially crippled by the increase, he has said two other things of note about the so-called Bank Rate.
First typical interest rate changes, increments, will be typically much smaller than the half of a percentage point that they used to be before the Crash of 2008 - so probably one quarter of a percentage point, or even possibly an eighth.
Also he has signalled that the new normal rate of interest over the medium term after a succession of rises over two or three years will be perhaps half the 4.5% over rate of the past 300 years. So nearer 2%.
Read Robert's blog in full here
Lydia Ko won the Canadian Women's Open to become the youngest tournament winner in LPGA Tour history.
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Bank of England governor Mark Carney has indicated that UK interest rates could rise "at the turn of this year".