Dr O'Donoghue has been made a Dame of the order of St Gregory the Great for her distinguished leadership of the Aboriginal community and her compassion for the vulnerable in society.
The Catholic Church said the Papal honours had also been conferred by Pope Benedict XVI.
Adelaide Archbishop Philip Wilson welcomed the honours.
"They are recognition of the faithful service of these men and women in the life of the archdiocese and an honour reflecting the entire Catholic community of Adelaide," he said.