Tasmanian senators Nick McKim and Vanessa Bleyer, as well as Western Australian senator Jordon Steele-John, crossed the floor to vote with the coalition in a bid to overturn the government's Improved Native Forest Management Instrument on Thursday.
But the majority of the party, including federal leader Larissa Waters, pledged to support the mechanism after "meaningful discussion" across the party.
The changes will allow state governments to earn carbon credits by blocking logging of existing native forests and selling the carbon sequestration credits to industrial polluters.
Senator Waters said the Greens negotiated measures to permanently strengthen logging restrictions and reduce the ability of coal and gas plants to use offsets to avoid reducing emissions.
"The Greens have secured important new protections for native forests, including a legal precedent to stop coal and gas using offsets, significantly reduce logging, and immediately protect forests," she said.
"The Greens party room has resolved to support the improved INFM because forest and habitat is critical to prevent endangered species from extinction as well as the climate."
With the majority of Greens senators voting with the government, the Nationals' motion to disallow the mechanism was struck down 34 to 27.
While Labor has strict prohibitions on crossing the floor and coalition frontbenchers are forbidden from going against shadow cabinet positions, the three Greens floor-crossers will face no repercussions, a Greens spokesperson confirmed.
Senator McKim and Senator Bleyer, who was only sworn in on Monday, said the vote was a "crossroads moment" for the party.
"We have not taken this decision lightly," they said in a statement.
The bill allows polluters to use carbon credits from the Great Koala National Park in NSW, which the state's premier, Chris Minns, warned would not be protected from logging unless the laws were passed.
"We have both spent many years of our lives fighting alongside activists and community groups to defend forests, and simply don't accept that forests need to be monetised in order to save them," Senators McKim and Bleyer said.
"This is a Labor shakedown. After repeatedly, unconditionally promising the Great Koala National Park, Labor is now holding koalas hostage and threatening to drive them towards extinction unless they can profit from their habitat."
Greens founder Bob Brown, as well as former leader Christine Milne, urged the party to vote against the bill.
"Unlike Labor, all environmentalists remain with the majority of Australians who want the forests and koalas saved for their own sakes," Mr Brown said.
But some environmentalists, as well as NSW Greens environment spokesperson Sue Higginson, begrudgingly backed the new carbon credit methodology.
"We applaud the Greens, crossbench and Australian and NSW government leaders who have shown courage and persistence to achieve this outcome," WWF Australia chief executive Dermot O'Gorman said.
