She said she would donate the AU$28,000 prize money to four organisations working for climate justice and helping areas already affected by climate change.
The prize was awarded before an audience of several hundred people and in the presence of several D-Day veterans, including France's Leon Gautier and US native American Charles Norman Shay.
Greta said she had spent an unforgettable day with Mr Shay on Omaha Beach, one of the sites of the 1944 Normandy landings that launched the Allied offensive that helped end World War II.
Paying tribute to their sacrifice, she said: "the least we can do to honour them is to stop destroying that same world that Charles, Leon and their friends and colleagues fought so hard to save for us."
Mr Shay said that young people should be prepared to "defend what they believe in."
"As a soldier, I fought for freedom and to liberate Europe and the world from Nazism 75 years ago."
"I'm deeply happy that you and the young generation fight for this noble cause," he told Greta.
Greta backs D-Day veteran call to fight "silent war"
Describing the challenges posed by climate change, Greta said seven million people died from illness related to toxic air pollution every year.
"This is a silent war going on," she said.
"We are currently on track for a world that could displace billions of people from their homes, taking away even the most basic living conditions from countless people, making areas of the world uninhabitable from some part of the year."
She said the "link between climate and ecological emergency and mass migration, famine and war was still not clear to many people" and urged change.
The Freedom Prize was set up to honour the values embodied by the Normandy landings. Its winner is chosen by a worldwide online poll of respondents aged between 15 and 25.
Greta beat out two other finalists, Saudi blogger and dissident Raif Badawi and Chinese photojournalist Lu Guang, to become the winner.