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Agzam Shergaziev (23) fired the hosts into the lead but Alexander Geynrikh restored parity in the 36th minute before giving the Uzbek League champions the lead in the 48th minute with his second goal. Odil Ahmedov (38) made the game safe for Pakhtakor.
Neftchi stayed a point behind Pakhtakor after destroying Tupalang 4-0. On the mark for Neftchi were Aziz Ibragimov (6), Akmal Holmatov (45, 48) and Ruslan Melzitdinov (55).
Kuruvchi were three off the pace after a 2-0 win over Andijan.
In other matches, Mashal made shortwork of Kyzylkum 4-0, Samarqand beat Traktor 2-1, Bukhara defeated Lokomotiv 3-1 and Nasaf edged Shurtan 1-0.
STANDINGS: 1. Pakhtakor 38, 2. Neftchi 37, 3. Kuruvchi 35, 4. Mashal 32, 5. Kyzylkum 28