The Young Socceroos inflicted the loss on the Junior All Whites, who are using the tournament to prepare for the FIFA under-20 World Cup in New Zealand starting on 30 May.
Australia, which hasn't qualified for the World Cup, sealed victory with two goals in five minutes to Alusine Fofanah and George Blackwood midway through the second half in Auckland.
New Zealand led 2-1 at halftime courtesy of goals to Clayton Lewis and Alex Rufer while Riley Woodcock scored Australia's first.
The Junior All Whites' next game is against Panama on Thursday. Australia meets Qatar on the same day, also in Auckland.
Ghana is the fifth team in a tournament which also features games in Hamilton.
