The deal will lead to Scottish Green co-leaders Patrick Harvie and Lorna Slater becoming government ministers – the first time any Green representative has held political office in a government in the UK.
First Minister and SNP leader Nicola Sturgeon announced the plans for the parties to work together, having agreed a “transformative” policy programme.
The deal was approved by Scottish Green party members at Saturday’s extraordinary general meeting (EGM) following a two-hour debate.
With proxy votes still to be counted, 715 members (88.5%) had backed the deal, 84 (10.4%) voted against and nine (1.1%) abstained.
The negotiations came over the summer after the SNP fell one seat short of an overall majority in May’s election.
The agreement on shared policies means the Scottish government will bring in another Scottish independence referendum before the end of 2023, if Covid-19 is under control by then, as well as environmental policies and a policies on rent controls.
Public disagreement between the parties will only be allowed on ten agreed topics, including aviation, green ports, direct financial support to businesses involved in the aerospace, defence and security sectors, field sports and the economic principles related to concepts of sustainable growth and inclusive growth.
Scottish Green MSP Ross Greer told party members at the EGM the list of subjects could be changed if further agreements or disagreements emerge.
Green co-leader Ms Slater said: “Scottish Green Party members are thoughtful and considerate, and I am pleased that having discussed and debated this agreement in great detail they have decided to take this historic step into government.
“The time has come for Scotland to step up efforts to decarbonise our economy and invest in a fairer, greener future.
“There’s no time to waste and I’m looking forward to start work on our transformative agenda in the coming days.”
Mr Harvie added: “I am delighted that our party members have given their support to this historic co-operation agreement that will see Greens enter government for the first time in Scotland, or indeed anywhere in the UK.
“With Greens in government, we will be able to deliver positive change for the people of Scotland.”
The draft powersharing agreement was announced by Ms Sturgeon and the two Scottish Green co-leaders at her official residence, Bute House in Edinburgh, last Friday.
Ms Sturgeon said: “I am delighted that members of both the Scottish Green Party and the SNP have agreed that we should work together in the Scottish Government to build a greener, fairer, independent Scotland.
“This historic agreement will provide a strong platform for the transformative programme we want to deliver.
“We will work collaboratively to support a fair recovery from Covid, address with urgency the impacts of the climate emergency, and give the people of Scotland a vote on independence.
“The agreement recognises that co-operation and consensus are essential to finding the practical solutions to the big challenges we face, and it echoes the founding principles of our Parliament.
“While our parties do not agree on everything, we have much common ground. We also have a determination – and indeed a responsibility – to look beyond our differences to build a better country.
“I look forward to working collaboratively with the Scottish Greens in government, and with all parties in parliament, to achieve this.”
The Scottish Conservatives called the deal a “coalition of chaos” focused on independence, while Scottish Labour said the “coalition of cuts” is a “disaster for Scotland”.
Scottish Labour leader Anas Sarwar said: “This coalition of cuts is formalising a long-standing agreement where Nicola Sturgeon and the SNP hammer our public services and the Greens nod along.
“This deal is all about the parties’ constitutional obsession and nothing to do with the climate emergency we should be focused on.
“The SNP is desperate to avoid scrutiny and this coalition with their Green branch office is simply designed to make it harder for parliament to hold the First Minister to account.
“Scottish Labour will focus on providing a real alternative that addresses our national recovery, protects the NHS and tackles the climate crisis.”