The Glasgow MSP was voted into the post by members alongside Edinburgh councillor Maggie Chapman, who succeeds Martha Wardrop in the role.
The two Scottish Green Party co-conveners will now lead the party as it campaigns for a Yes vote in next year's independence referendum and as it prepares for the 2014 European elections, with Ms Chapman the lead Green candidate for that vote.
Mr Harvie said: "Maggie Chapman will build on the good job Martha Wardrop has done in the role and we'd all like to thank Martha for her work. Our eyes are firmly on getting Scotland its first Green MEP and securing a Yes vote in the independence referendum."
Ms Chapman, a lecturer at Edinburgh Napier University who is originally from Zimbabwe, said: "With the independence referendum less than a year away, we need to raise our voices for a different kind of Scotland.
"We need to stand up to Westminster politicians who are trying to shift blame for our economic woes off bankers and onto immigrants, off the rich and onto the unemployed.
"I'll be campaigning for a Scotland that's run for people, not for profit; that hands power to communities, not to corporations.
"To win the referendum, it's going to be crucial that Greens inspire people with a vision of a different kind of Scotland - where we build an economy which pays work properly and respects carers, where we see public services as the bedrock of our civilisation; where we put equality ahead of greed."