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Maksim Shatskikh put the visitors ahead on 27 minutes before Keiji Tamada responded in the 40th minute.
Uzbekistan scored its first goal and earned the first point in the fourth round of 2010 World Cup Asian Zone qualifiers.
The results see Australia lead Group 1 on six points from two games, Japan and Qatar level on four points with Bahrain and Uzbekistan on a point apiece.
The top two teams in each group earn direct qualification to the 2010 World Cup finals in South Africa with the third place teams squaring off in a play-off.