The site near the town of Kimba will store low-level waste permanently and intermediate-level waste temporarily.
It will employ about 45 people and the government will gift the community a $31 million package.
A property at Lyndhurst, also near Kimba, had been in the running but Mr Canavan said the Napandee proposal had more support.
"The facility has broad community support in Kimba but I acknowledge there remains opposition, particularly amongst the Barngarla People and their representative group," he said.
"We will work with traditional owners to protect culture and heritage, and to maximise economic opportunities and outcomes for local Aboriginal communities near the future facility."
Before the announcement, Peter Woolford, president of the No Radioactive Waste on Agricultural Land in Kimba or SA committee, said locals and visitors will rally against the project on Sunday.
Mr Woolford says five years of consultation has taken its toll on the town and his group is calling on the federal government to abandon both sites.
"The process the federal government has undertaken to find a location for this facility has been a long and arduous one for the Kimba community," he said.
The Australian town divided over hosting the country's first nuclear waste dump
"Matthew Canavan's process has been arbitrary, completely lacking in clarity and an extremely divisive process.
"It is time for him to acknowledge that the prerequisite of 'broad community support' does not exist in Kimba, and allow the community to move forward."
The dump is opposed by environmental and indigenous groups - but a recent poll conducted around Kimba returned a 62 per cent vote in favour of the facility.
Jeff Baldock, who owns the Napandee site, said the project was an opportunity for the area to secure its future.
"It's very rare that a small country community gets the chance to guarantee that it's still going to be here in 300 years time," he said.
"We're always looking for ways to attract new industry and try and boost our local community.
"This is one of those projects that is not only supplying us with jobs but with an opportunity to attract new industry."
The Department of Industry, Innovation and Science said it had provided a significant amount of material to inform the site decision.
"The department has put the community at the centre of this process, which involved more than four years of deep consultation and technical assessments," it said.
Guest speakers at Sunday's rally will include local Labor MP Eddie Hughes, Conservation Council of SA chief Craig Wilkins and Kimba farmers James Shepherdson and Tom Harris.