Sister Patricia Fox was escorted to the airport by about 200 human rights activists who praised her years of service in the impoverished Southeast Asian nation and condemned the administration for forcing her to leave.
"Duterte, expel him, Sister Pat, bring her back," some of the rallyists chanted.
Fox - who has spent almost three decades working with Philippine labourers, farmers and urban poor - said she was leaving with sadness but urged her sympathisers to continue helping the disadvantaged.
"I hope (Duterte) listens to the voice of the little people, not just the military, not just the businessmen, but the farmers, the workers, the tribal folk," she said in a pre-departure press conference.
Fox apparently angered the fiery president by joining a fact-finding mission in April to investigate alleged abuses against farmers, including killings and evictions by soldiers fighting guerrillas in the southern Philippines.
She was arrested briefly on charges of violating her visa's terms against activism and the slow turning wheels of the Philippine bureaucracy began moving to strip her of her papers.
Immigration authorities earlier this week refused to extend her tourist visa and ordered the 71-year-old out by Saturday.
She decided to return to Australia rather than risk being forcibly removed.
The country's Catholic leadership, which counts about 80 percent of Filipinos as followers, bemoaned her scheduled departure, saying "Sister Patricia Fox's deportation is a blow to the missionary spirit of the church".
"The faith she proclaims is not detrimental to the life of Filipinos. In fact, it is a source of hope and consolation to our suffering countrymen," said Father Jerome Secillano, executive director of the bishops' media affairs office.
However Duterte's spokesman Salvador Panelo said: "The departure of Sister Patricia Fox is a timely reminder to all foreigners who stay or sojourn in this country that they are not entitled to all the rights and privileges granted to the citizens of the Philippines".
Church figures have previously criticised Duterte's policies particularly his signature anti-drug campaign that the government has left almost 5,000 people dead since Duterte took office in 2016.
Human rights groups charge that the actual death toll is about five times that total.
Duterte in turn has deeply resented criticism from the Church, particularly outsiders, attacking Fox and others in a speech in June, saying "those foreigners who have no reason to meddle, they come here, those sons of whores, you priests... you nuns".