The prime minister said the number of Australian Defence Force personnel in Afghanistan had been drawn down from a height of more than 1500 to just 80 troops.
The remaining soldiers will slowly depart within months, drawing the 20-year military mission to a close.
Mr Morrison choked back tears as he read the names of 41 ADF troops killed while serving in Afghanistan.
"These brave Australians are amongst our greatest ever, who have served in the name of freedom," he told reporters in Perth on Thursday.
"We thank them for their service humbly and gratefully."
Australia has had 39,000 troops rotate through Afghanistan at some point over the conflict.
The prime minister was asked whether it was worth going into Afghanistan, given the cost to Australian lives.
"Freedom is always worth it," he said.
Mr Morrison declined to comment on alleged war crimes committed by Australian troops in Afghanistan, or whether the ADF could have done better.
"There will be time to talk about those things. Today is not that time."
He acknowledged the conflict had exacted an enormous toll on the people of Afghanistan, and the complex task of making peace still lay ahead.
"Australia continues to support the peace negotiations between the Afghan government and the Taliban. We encourage both parties to commit to the peace process and call on the Taliban to cease the violence," he said.
The prime minister said while Australia's military contribution would reduce, the country would continue to support the stability of Afghanistan through diplomacy, development programs and people-to-people links.
"Australia remains committed to helping Afghanistan preserve the gains of the last 20 years, particularly for women and girls," he said.