Commemorative services will be held around the country on Friday, including at the Australian Forces National Memorial in Canberra.
Veterans' Affairs Minister Matt Keogh will deliver the address and will represent Anthony Albanese.
Governor-General David Hurley will pay his respects alongside Vietnamese Ambassador to Australia Nguyen Tat Thanh.
A flypast of Vietnam-era aircraft will take place as part of the service by the Historical Aviation Restoration Society.
In Melbourne, a service to mark the anniversary will be held at the Shrine of Remembrance.
About 60,000 Australians served in the Vietnam War, with more than 3000 wounded and 523 killed.
Returning home from Vietnam, veterans experienced hostility from the community over their involvement in an unpopular conflict, which included being spat on and having paint thrown on them during parades.
The prime minister, who is in Brisbane for the Australian Labor Party Conference, will attend a commemorative service in Ipswich.
Mr Albanese paid tribute to their sacrifices and apologised it took the nation as long as it did to recognise them.
"Their experiences during and after the war are a powerful reminder of the sacrifices made by those who have served our country and the debt of gratitude we owe each and every one of our veterans," he said.
"It is important as Australians we know the stories of service in Vietnam and what our veterans faced when returned home."
Mr Keogh said when defence personnel were returning home from Vietnam, many felt unsupported and unrecognised.
"In marking 50 years since the end of Australia's involvement in Vietnam, we honour and thank all those who served, and the sacrifices of their families," he said.
It's estimated there are more than 35,000 Australian veterans of this war who are still living, with most aged 70 or older.
