The state government has negotiated with the opposition in "good faith" over amendments to the GM Bill to allow it to pass for growers to plan their 2021 growing season.
The bill passed the Lower House on Tuesday evening, and may be debated in the Upper House this week.
Minister for Primary Industries and Regional Development Tim Whetstone said the government had agreed to amend the Genetically Modified Crops Management (Designated Area) Amendment Bill 2019 so that local councils will have the time-limited ability to apply to be a GM free crop cultivation area.
The amendment means councils will be able to apply to have the moratorium continue within their district however the final decision will come from the Primary Industries minister.
Local councils will have six months to apply after the legislation is passed, however the moratorium will remain on Kangaroo Island.
"This agreement is a great outcome for South Australian farmers who will have the opportunity to reap the benefits of growing GM where that is best for their business," said Mr Whetstone.
"The legislation will provide farmers with the regulatory certainty they need to invest in GM seed and plant GM crops in time for the 2021 grain growing season.
"After 16 years and millions of dollars in lost economic and research opportunities, it is a historic day for farmers in this state who can look forward to the choice in what they want to grow.
"Lifting the moratorium will not only provide economic benefits for our farmers but it will put South Australia on a level playing field with every other mainland state in Australia which has had access to GM technology for at least a decade."
Grain Producers South Australia chief executive officer Caroline Rhodes said it may present an opportunity to break the "political deadlock" on GM crops.
"This bipartisan compromise will hopefully serve as an orderly transition towards removing restrictions on GM crops in SA," she said.
"Under the proposed framework, the final decision on GM-free zones will still reside with the Minister for Primary Industries and Regional Development.
"While Labor's proposed framework is not in absolute alignment with GPSA's preferred policy position, this model may represent an acceptable compromise to enable the commercial cultivation of GM crops from 2021."
A motion in parliament in November 2019 blocked regulatory changes to immediately lift the ban in time for the 2020 growing season, after it was argued the government was side-stepping parliamentary due process.
Earlier this month the Greens announced they would move to reinstate the GM ban when parliament resumed today, April 28.
The Greens today labelled the move of support from Labor to the state government's bill as a "major betrayal".
"This is a sudden reversal of their long-held policy and 2018 state election platform in support of the GM crops moratorium," said Green member of the legislative council Mark Parnell.
"In a cruel twist, Labor has held out the forlorn hope that individual local councils can still remain GM-free, however the final decision rests with the minister who is free to ignore local concerns and allow GM crops to be grown virtually anywhere.
"Cash-strapped councils only have six months to consult their communities with no additional funding and no assurance that their views will prevail."
Member for Flinders Peter Treloar said while the amendments were a compromise, he expected many councils across the broadacre farming areas in the state would be pleased to give their farmers the choice.
"I was pleased to contribute to the parliamentary debate, I had indeed lost count of the number of times I have spoken about this issue in the state Parliament over the years," he said.
"It is great news for our farmers and regional communities, who for a long time have been calling for the opportunity to have a choice."