Ghislaine Landry's try with one minute remaining put Canada ahead for good after a back-and-forth final. Canadian captain Jen Kish retrieved the ensuing kickoff to end Australia's hopes of a comeback.
"They've been playing some great rugby, I'm so proud of them," said Canadian coach John Tait.
"We capitalized on their mistakes and we stuck together," said Kish. "I think that was what got us the victory."
After receiving their medals, the Canadian women celebrated on the field to the sounds of "Happy" by Pharrell Williams.
Sunday's Cup final was a rematch of last week in London, where Australia scored three late tries to defeat Canada 20-15. Amsterdam was the last event of the six-stop women's circuit.
It marked the first time the Canadian women had made it to two finals in the same season. They had lost their two previous final appearances, both to New Zealand.
Karen Paquin, set up by Kish after she drew in two defenders, made it 5-0 in the first half of the final. But the Australians pulled ahead 7-5 on a converted try as Sharni Williams ran though the Canadian defence.
Magali Harvey restored the Canadian lead, flying down the wing to make it 10-7 at the half.
Speedster Emma Tonegato put the Aussies back in front 12-10. But Paquin outpaced the opposition to make it 15-12. Landry hit the post, missing the conversion.
Tonegato beat a Canadian defender and raced the length of the field for a 17-15 Australian lead before Landry, the leading scorer on the circuit this season, decided the matter.
A stingy Canadian defence helped pave the way for success in Amsterdam. The Canadians gave up just 29 points in five games en route to the final. Australia yielded just 14 points.
The top four teams in the overall standings at the end of play Saturday automatically qualified for the 2016 Games.
Series leader New Zealand booked its ticket to Rio last week in London. The Canadians and Australians were informed they had secured Olympic qualification midway through competition Friday.
The final berth was decided in the third-place playoff Saturday when England edged the U.S. 15-14.
New Zealand finished first in the standings with 108 points ahead of Canada (96), Australia (94) and England (76). England will qualify Team Great Britain for the Olympics.
The English came into the tournament in sixth place with 60 points, two behind France and the U.S., who were both on 62.
New Zealand won the Series overall title for the third year in a row just by showing up in Amsterdam.
But the Kiwis wobbled for the second week in a row.
After winning the first four stops on the tour with a perfect 36-0 record, the New Zealand women lost four games in the final two tournaments. On Saturday they were beaten 17-14 by England in the quarter-finals and had to settle for fifth place after defeating France 35-5 in the consolation Plate final.
The Kiwis finished third in London last week.
Canada made short work of the French in the quarter-finals, winning 33-0 on tries by Sara Kaljuvee, Mandy Marchak, Landry, Paquin and Ashley Steacy. Landry and Harvey added two conversions apiece.
The Canadians, in a matchup of unbeaten teams, downed the Americans 190-14 in the semifinal.
Landry scored an intercept try, her sixth try of the weekend. After the Americans tied it up, Harvey put Canada ahead, using her speed to gather in a Landry kick for a 12-7 lead at the half. A Paquin converted try made it 19-7.
The Americans, taking advantage of Landry in the sin-bin, closed to 19-14 with less than two minutes remaining. But Landry made a saving tackle with American Lauren Doyle charging for the goal-line to preserve the win.
Australia defeated Russia 31-0 and England 26-0 to make the final.
Fiji, South Africa, New Zealand and England have already qualified for the men's Olympic field.
The 12-country Olympic fields will be filled out by regional qualifying tournaments and a world repechage competition. Host Brazil does not need to qualify.
The Canadian men will have to get past the surging U.S. Eagles at the North American qualifying event in June in North Carolina.