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Tachmurod Agamuradov side scored only goal of the match in the 27th minute. Farrukh Shotursunov was on target for the Uzbek club.
Despite victory, Pakhtakor youngsters failed to qualify to play-offs. Both Empoli and Pakhtakor collected five points, but Italian has better goal difference.
Another Italian club Arzenas claimed the third place with 3 points, while Honved was the fourth with a point.