About 100 Brazilian fans were waiting at Vitoria airport but the Socceroos, arriving in darkness, went straight from their plane to a bus with blacked-out windows and were whisked away to their hotel.
Dozens of heavily armed riot police were also at the airport, with authorities apparently fearing a repeat of protests which have marred the tournament's build-up.
Fans trying to catch a glimpse of the squad, who were wearing suits, rushed into the street to wave as they set out on the short drive to their town-centre hotel.
They are ranked at 59, the lowest of the tournament, with one columnist remarking "the bookmakers regard Australia's World Cup possibilities as something worse than a snowball's survival chances in hell".
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But midfielder Tommy Oar said Ange Postecoglou's side were using their lowly status as motivation.
"We are the underdogs. It will be a good opportunity for the Australian team to surprise, so this is all very exciting. And being in the 'soccer country' is an extra motivation, of course," Oar said in a statement released by FIFA.
The next teams expected in Brazil are Croatia and Iran on June 3. The last arrivals are South Korea, Ghana and Portugal on June 11, the day before the opening match.
Meanwhile hosts Brazil opened their base camp on Monday and, after undergoing medical checks, took to the practice pitch for the first time on Wednesday.
Brazil has been hit by a wave of strikes and protests in recent weeks sparked by public anger over the more than USD 11 billion being spent on the tournament in a country with urgent education, health and transport needs.