The soldier from the Sydney-based Second Commando Unit was found by his colleagues in an admin building in Kabul overnight, Chief of the Defence Force Mark Binskin says.
He was rushed to a medical facility for treatment.
"Sadly the soldier's injuries were too severe and he later died surrounded by his mates," Air Chief Marshal Binskin told reporters in Canberra on Wednesday.
It was believed to be a "non-combat related incident", he said.
The Australian Defence Force has offered its condolences to the family of the soldier.
"He was a highly-qualified, experienced and well-respected special forces soldier," Air Chief Marshal Binskin said.
"His death will impact the nation."
Coalition military police and the ADF's investigative service have begun collecting evidence from the site.
Air Chief Marshal Binskin said the ADF did not yet have all the facts so it was inappropriate to speculate further on the details or circumstances surrounding the incident.
He declined to reveal any personal details about the man, or say how many tours he had done in Afghanistan.
A psychological support team has been deployed to assist the man's colleagues.
Asked about post-traumatic stress disorder in the defence force, Air Chief Marshal Binskin said: "I am confident in what Defence does in the mental health space."
Australia currently has about 400 defence personnel in Afghanistan.
Readers seeking support and information about suicide prevention can contact Lifeline on 13 11 14 or MensLine Australia 1300 78 99 78.
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