Acting Prime Minister Wayne Swan says the move represents a key achievement for Australia's term as Commonwealth chair, which ended last month.
The charter was a key recommendation of a group of eminent people, including former Australian High Court judge Michael Kirby, who called for urgent reform of the 54-nation body to keep it relevant.
Leaders agreed to adopt the charter at the Commonwealth Heads of Government (CHOGM) meeting Prime Minister Julia Gillard hosted in Perth last October.
The charter aims to enshrine the values of the Commonwealth, which is mostly made up of former British colonies, into a single document.
The charter emphasises democracy, human rights and the rule of law.
It also seeks to promote tolerance, freedom of expression, the separation of powers, gender equality and environmental sustainability.
Commonwealth Secretary-General Kamalesh Sharma said the charter would be a defining document for the group.
"We are now better placed to respond to the needs of our citizens," he said in a statement on Thursday.
Commonwealth countries have a combined population of more than two billion.
Fiji was suspended from the Commonwealth in 2006 after Commodore Frank Bainimarama seized power in a coup. It remains suspended pending promised 2014 elections.