Legislation to lift the Genetically Modified crop moratorium on mainland South Australia passed parliament on Wednesday.
Minister for Primary Industries and Regional Development Tim Whetstone said it was an "historic" day for farmers.
"South Australian farmers have been looking forward to this day for nearly two decades," he said.
"Now the legislation has passed parliament our grain growers have the certainty they need to invest in GM seed and plant GM crops in time for the 2021 grain growing season.
"Lifting the moratorium will bring South Australia into the 2020s and put our farmers on a level playing field with their counterparts around the country who have had access to GM technology for at least a decade."
The state government negotiated with the opposition last month, coming to a compromise to allow the GM bill to pass.
The amendment was introduced on April 28 and passed the Lower House later that day, and was passed into legislation in the Upper House yesterday.
The state opposition negotiated an amendment to the bill which will give councils six months to apply to have the moratorium continue within their district however the final decision will come from the Primary Industries minister.
Councils will have to prove financial advantage to keeping the ban.
The moratorium will remain on Kangaroo Island.
Grain Producers SA chief executive officer Caroline Rhodes said the bill now established a "level playing field" for SA growers with the rest of the nation's farmers.
"GPSA has been steadfast in its advocacy for freedom of choice and has worked tirelessly behind the scenes to reach this outcome and to support the political deliberations of both the government and opposition," she said.
"While the amended bill is not in absolute alignment with GPSA's preferred policy position, we believe this compromise model was the best opportunity to provide certainty for the industry in time for the 2021 season.
""We thank Tim Whetstone for his commitment to seeing this historic reform through.
"We also thank shadow minister Eddie Hughes for listening to South Australian growers and working with GPSA and the government in order to bridge the political divide so we could reach this point.
"We...look forward to growers finally being able to make their own choices about which crops they want to grow without the hindrance of legislators on North Terrace."
Australian Seed Federation general manager Osman Mewett said politics will no longer stand in the way of SA farmer's being able to innovate.
"The GM crop moratorium has restricted the incentive for South Australian researchers to develop agricultural bio-technologies for South Australia," he said.
"The GM seed transport ban had a significant negative impact on the Australian seed industry, resulting in increased costs to seed producers and long delays from having to use other transport measures to divert genetically modified seed around South Australia.
"In addition to the strong leadership shown by Premier Marshall and Minister Whetstone, I commend opposition leader Peter Malinauskas, and shadow minister for primary industries Eddie Hughes, for putting party politics to the side and delivering a way forward that will benefit all South Australians."
Moves to lift the GM ban have been ongoing, when 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.