The 29-year-old, a serving captain in the British Army, joined the families of fallen members of the Special Air Service Regiment (SASR) to lay wreaths in the Garden of Reflection at the unit's Campbell Barracks in Perth.
He flew into the Western Australian city accompanied by the country's Prime Minister, Tony Abbott, after a pop star-like reception in Sydney on his first state visit to the country.
He met and had lunch with present and former members of the unit and toured the base before flying to Dubai for a fundraiser for his Sentebale Aids charity.
The SASR's commanding officer, whose identity was only given as "Lieutenant Colonel G", said: "It has been 10 years since Prince Harry last visited Australia and we are humbled and grateful that he has made the time to join us. Prince Harry knows what it means to serve his nation on operations and most importantly what it means to the families of those serving.
"The visit by His Royal Highness and the Prime Minister represents a unique opportunity to recognise the broader SAS regimental family that provides back-up and support at home.
"Families play a critical role for those serving in the SASR, and indeed the whole of the Australian Defence Force, and we are thankful that the families of some of our serving, former and fallen members were able to be here."
Harry also met members of groups including the SAS Resources Fund, the SAS Association, the SAS Historical Foundation and the SAS Auxiliary, all of which provide support to the unit and its members.
Harry's visit to Australia lasted barely 36 hours.
The Prince arrived in Australia late on Friday for the whistle-stop tour, his first official visit to represent the Queen in the country he first visited 10 years ago.