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Uzbekistan champions conceded a goal after just 40 seconds. Esam Dhahi opened the score in the match.
Pakhtakor midfielder Kahi Maharadze scored equalizer on 19 minutes, scoring from penalty-kick.
On 65 minutes, Kahi Maharadze netted an own goal to give all three points to the UAE club and tickets to play-offs.
Lekhwiya topped the Group B after a 2-0 victory over Al Ittifaq with 11 points. Al Shabab clinched second place after victory in Tashkent with nine points. Al Ittifaq and Pakhtakor have seven points.