Energy and Mining Minister Tom Koutsantonis said Terramin Australia's application to develop the Bird In Hand underground mine at Woodside had been rejected after a comprehensive assessment.
Mr Koutsantonis said while Terramin's proposal satisfied statutory obligations and the proposed mine would have had a short life, the potential impact on surrounding businesses, including world-class wineries and associated regional tourism could have longer-term implications.
"This is not a decision I've taken lightly or easily," the minister said on Thursday.
"The area of the proposed mine is home to a world-class viticulture industry, producing some of Australia's best-loved wines.
"Tourism to the region is a critical contributor to the local economy and, on balance, there remains a possibility this proposed short-term mine may adversely affect the established and significant long-term agricultural and tourism industries."
Terramin Australia said its board and management were surprised and disappointed by the decision.
"The applications were supported by comprehensive studies based on science, which demonstrated that there would be no adverse environmental outcomes arising from Terramin's mining proposal," the company said in a statement to the Australian Stock Exchange.
"The gold deposit is extremely high grade and would have been extracted through an unobtrusive, single keyhole entry method, with all surface activities well within the boundaries of Terramin's land, with any mine infrastructure largely hidden from view by extensive tree stands and vegetation."
Terramin said the decision also meant that the local Woodside and Strathalbyn communities would miss out on the creation of more than 140 highly paid mining jobs and many more indirect jobs while SA would lose the mine's significant economic contribution to the state economy.
But Premier Peter Malinauskas said there was not much sense in creating some jobs at the expense of others.
"That's a balance that we have to get right," he said.
"There is no doubt that mine would have created jobs, but it would also have cost others in an industry that reputationally is profoundly important ... the wine industry."
The government's decision was welcomed by Adelaide Hills independent state MP Dan Cregan and his federal counterpart Rebekha Sharkie, who said the prospect of a goldmine operating in some of SA's best agricultural and viticultural land had caused much angst and distress in the community.
SA Chamber of Mines and Energy chief executive Rebecca Knol said the decision had been made on "populist political grounds".
"This decision represents a missed opportunity for the state at a time when critical minerals are in high demand," she said.
