Delegates at the extraordinary congress voted 93 percent in favour of the agreement signed on Thursday by Greens chief Werner Kogler.
“Europe is watching us and what we do is important on a continent-wide basis,” Kogler said, adding that he was delighted to be able to “bury fossil fuels” and achieve “carbon neutrality”.
The new coalition government with the conservatives, led by Sebastian Kurz, is expected to be sworn in next week.
The two parties announced late Wednesday that they had agreed to govern together after key election gains in September following a corruption scandal that broke apart Kurz's ruling coalition with the far right.
On Thursday they announced that the coalition would aim for carbon neutrality by 2040 to make the country a European “forerunner” in climate protection.
Party members gathering in Salzburg admitted that they would have to “swallow snakes” to find common ground. “We must not forget that we are a party that polls 13.8 percent,” delegate Birgit Hebein said.
The Greens will have four ministers in the new government, against ten for the conservatives.