Members of the 3rd Battalion of the Royal Australian Regiment Task Group were welcomed home in Brisbane and Townsville on Saturday.
The 750 men and women had been deployed in Oruzgan province in Afghanistan, training troops for the Afghan army.
But Major General Stuart Smith said the deployment came at a high cost to the battalion.
Lance Corporal Stjepan Milosevic, Sapper James Martin and Private Robert Poate were killed by a rogue Afghan soldier they were training.
AAP reports all Australian troops are to withdraw from forward operating bases in Uruzgan by the end of this year, leaving troops at Tarin Kowt, Kandahar and Kabul.
The Special Operations Task Group will continue to operate until 31 December, 2014.