Hertha Berlin winger Mat Leckie opened the scoring for Australia at the half hour mark, and proceeded to sandwich a first international goal from Andrew Nabbout.
Milos Degenek further compounded the thrashing to 4-0 after forcing Czech international Jakub Jugas into an own goal in the 80th-minute.
The fixture marked the last chance for members of the Australian squad to prove their worth, before manager Bert van Marwijk is forced to cut his side down into the World Cup 23-man team.
After the match, Van Marwijk said he was ''satisfied'' with his players' performance. He added: ''When you win it's always better. It's good for the confidence. It helps and it is also important for individual players.''
The win signified Australia's first win away from home since September of 2016, and will likely be a huge confidence boost as they fast approach their World Cup opener against France.