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The sides left the pitch scores after the first half despite the sides have good chances to score.
Bakaev scored within a minute of the start of the second half to open the scoring and converted a cross of Hasan Juraev from the left to make it 2-0 three minutes later.
Jordan replied quickly, however, when captain Bashar Bani Yaseen smashed home from close range in the 58th minute but they could not find the equaliser as the Uzbeks closed out the match looking the most likely to score again.
Uzbekistan will face winner of the match between Australia and Iraq.