A separate vote among the estimated 120 delegates put the party on a conflicting path to Yes Scotland by continuing support for a multi-option referendum. The campaign group wants a straight Yes-No ballot, a plan which is also backed by the UK Government and senior SNP figures such as Nicola Sturgeon.
In a statement following the overwhelming vote to join Yes Scotland, Mr Harvie said: "Today's decision ensures that Greens take a front-row seat in this exciting debate, promoting fresh and radical ideas on Scotland's future.
"Greens are not nationalists, and we're not motivated by devotion to one flag or the other. But we can see huge opportunities to make our country fairer and greener. We look forward to working with Yes Scotland to set out a transformational vision for Scotland's society, economy and environment, and building a campaign to win.
"Greens are clear in our steadfast opposition to Scotland remaining in the Nato nuclear club and committing billions of pounds on an outdated approach to defence. Over the next two years, we will argue for a vision of Scotland as a peaceful country with social justice, equality and environmental protection at its core."
There were clear divisions of opinion, with former leader Robin Harper voting against the plan after saying he is not "gung ho" for independence.