A brace from Jose Luis Villanueva steered the defending champions to their 14th consecutive win and they lead second-placed Pakhtakor, who beat Mashal 3-0, by six points in the 16-team standings.
Kamoliddin Murzoev restored parity for Nasaf in the 12th minute from the spot after the Chilean put Bunyodkor ahead in the eighth minute. Villanueva scored their match-winner a minute from the half hour mark.
Bunyodkor will host Korea Republic’s Pohang Steelers in the first leg of their AFC Champions League quarter-finals on September 23 before travelling to Korea for their return leg a week later.
Alexander Geynrikh (two) and Zaynitdin Tadjiev were on target for Pakhtakor who will face Saudi Arabia ’s Al Ittihad in the two-legged ACL quarter-finals on September 24 and 30.
AFC Cup quarter-finalists Neftchi were held 1-1 by Navbahor when Alisher Halikov’s 12th minute opener for Neftchi was cancelled out by Ilkhom Boydedaev in the 79th minute.
Neftchi will play Hong Kong’s South China in the continental quarter-finals on September 15 and 30.
Bunyodkor will now face archrivals Pakhtakor on July 12 in their postponed 11th round match.