Both teams had already qualified for the final round of regional qualifiers but Aleksandr Shadrin's 54th-minute strike condemned hosts Japan to a second successive defeat.
"We were in control in the first half and should have taken our chances," Japan coach Alberto Zaccheroni told reporters.
"Uzbekistan showed real quality after the break. We've got to be ready for the final round now. We have three months to get ourselves in the best possible condition."
Shinji Okazaki went closest for Japan, hitting the bar in the first half, but a below-strength Uzbekistan deserved victory for their enterprise in freezing conditions.
The final whistle was greeted by jeers from fans puzzled over Zaccheroni's decision not to send on Bolton Wanderers winger Ryo Miyaichi as a substitute after giving the teenager his first call-up.
"The fact we lost says it all," said captain Makoto Hasebe. "It's a tough pill to swallow but we have to put things right and step up a level in the final round of qualifying."
The draw for the final round takes place on March 9.
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