Defender Nick Ansell headed home the only goal for Kevin Muscat's side, who beat Italian champions Juventus on penalties last week.
Atletico boss Diego Simeone, who selected seven academy players, was pleased with his side's performance.
"I take from this many positive things," he said.
"The youths are learning and this is the way to improve."
Atletico will return to Spain on Tuesday before facing Galatasaray in Turkey  on 6 August as part of their pre-season preparation.
Champions League finalists Atletico Madrid lost 1-0 to A-League side Melbourne Victory during their pre-season tour of Australia.