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The victory took Ravshan Haydarov’s charges on top of the standings with six points from two games, followed by AFC Cup side Nasaf also on six points.
Dilshod Sharofetdinov scored the match-winner for Pakhtakor three minutes before half time.
Pakhtakor, who were held 2-2 by Saudi Arabia’s Al Nassr at home in the continental opener last week, will travel to Doha to meet Al Sadd on March 16.