The Yankunytjatjara woman played a key role in the 1967 referendum, lobbied the Keating government to recognise Indigenous land ownership through the native title laws and advised on the apology to the stolen generation.
She died on February 4 aged 91 on Kaurna Country in Adelaide with her immediate family by her side.
South Australian Premier Peter Malinauskas announced Dr O'Donoghue would be honoured at a state funeral on March 8.
"Through her lifelong work, Dr O'Donoghue has made an incredible contribution to the betterment of our country and people," Mr Malinauskas said on Tuesday.
"(She) leaves a legacy of strong advocacy, passion and dedication."
Dr O'Donoghue gained prominence after becoming the first Aboriginal person to train as a nurse at Royal Adelaide Hospital in 1954.
She had been denied the opportunity because of her Indigenous heritage and her successful lobbying was just the beginning of a career fighting for equality.
Prime Minister Anthony Albanese described her as one of the most remarkable leaders the country has known.
"Dr O'Donoghue had an abiding faith in the possibility of a more united and reconciled Australia," he said after her death.
She was a member of the stolen generation, taken from her mother at two and put in a children's home.
In the 60s, she joined Aboriginal rights groups in South Australia before working as a nurse and welfare officer for the Department of Aboriginal Affairs in the same state.
She campaigned for the 1967 referendum which changed the constitution to count Aboriginal and Torres Strait Islander people in the population and make laws for them.
Dr O'Donoghue continued her advocacy and was later made a member of the Order of Australia in 1977.
She was the founding chairperson of the National Aboriginal Conference, and in 1984 was named Australian of the Year.
Dr O'Donoghue became the inaugural chairperson of the Aboriginal and Torres Strait Islander Commission in 1990.
One of her greatest achievements was lobbying the Keating government to recognise Aboriginal land ownership through the Native Title Act.
Another was advising then prime minister Kevin Rudd on the apology to Aboriginal and Torres Strait Islander peoples, particularly the stolen generation, in 2008.
The non-profit Lowitja O'Donoghue Foundation was set up in 2022 to continue her legacy.
The state funeral will take place at 1pm at St Peter's Cathedral, on Kaurna Country in North Adelaide.
