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The quarter-final will be played on Wednesday.
Bahodir Nasimov scored both the goals for the Uzbekistan champions’ reserves side.
MTTU lost to group leaders Ukraine’s Dynamo Kiev but qualified for the last eight as the Russian Select team, who finished second, had only academic interest in the competition.
Two-time AFC President’s Cup champions Kyrgyzstan’s Dordoi-Dynamo were held 1-1 by Latvian outfit Metallurg with Aleksandr Mysikov scoring for the Central Asians.
Tajikistan’s Vakhsh played a 1-1 draw with Finland’s HJK. Rustam Usmanov scored Vakhsh’s goal.