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Zahid Abdullaev scored either side of half-time to put the home side in control at 3-1 before Bahodyr Nasimov reduced the deficit for Samarqand three minutes before the hour mark.
Shuhrat Yuldashev quickly restored Metallurg’s lead, and after an own-goal from Bahodyr Nasimov with nine minutes remaining secured the win, David Onia grabbed a late consolation for Samarqand.
Metallurg’s third win in 20 games this season lifted them off the foot of the table above Mash’al and Bukhara into 14th, while Samarqand remained ninth.