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Joao Victor put the defending champions ahead eight minutes before the breather and Anvar Soliev made it 2-0 immediately after the restart to give their side fourth victory in as many games.
Pakhtakor, Uzbekistan’s another representative in the continental championship, will play their fourth round game against Nasaf on 29 April. Pakhtakor are leading ACL Group A with four points and will face Iran’s Saba Battery on Tuesday.
In other matches, Khorezm beat Kyzylkum 2-0, Almalyk overcame Dynamo 1-0, Shurtan beat Sogdiana 2-1, Bukhara played a goalless draw with Metallurg and Andijan held Navbahor 1-1.
STANDINGS: 1. Bunyodkor 12, 2. Nasaf 9, 3. Khorezm 8, 4. Sogdiana 7, 5. Lokomotive 7.