Australia, who have two more matches to play in Group A of the final Asian qualifying phase, have 14 points from six matches.
The Socceroos struggled in hot conditions as the Qataris went for broke but they maintained their record of not conceding a goal in the final qualifying phase.
Earlier, Shinji Okazaki headed the early goal which secured Japan's berth at the World Cup for the fourth time in a row.
Makoto Hasebe was sent off for elbowing Uzbek captain Server Djeparov with two minutes remaining but Japan held on.
Japan coach Takeshi Okada said: "We played according to our plan and clinched a very important win.
"I'm very pleased with my players' performance in the match. They played with heart but it was a very well-disciplined performance."
Okada's Uzbeki counterpart Mirjalol Kasymov congratulated Japan and added: "We did all we could do today. We have nothing to reproach ourselves about."
Danny Jordaan, the 2010 organising committee chief in South Africa said: "Japan are a big team - both on and off the field - who have become a major force in world football. We are delighted that they today became the first team to qualify for the 2010 Fifa World Cup."
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