Muidin Mamazulunov scored the match-winner for Almalyk in the stoppage time as the AFC Champions League semi-finalists remained on 39 points with a match in hand.
Bunyodkor thrashed Metallurg 4-1 to take their tally to 54 points.
Anvar Soliev opened the scoring for Bunyodkor, who will face Korea Republic ’s Pohang Steelers in the ACL quarter-finals next month, while Rivaldo doubled the advantage from the spot at the half hour mark.
AFC Player of the Year Server Djeparov (74) and Joao Victor (86) added two more goals for Luiz Felipe Scolari’s side while Bojan Kolevic reduced the deficit for Metallurg.
In other matches, AFC Cup quarter-finalists Neftchi crushed Sogdiana 7-0, Bukhara lost to Lokomotive 3-2, Andijan beat Shurtan 2-1, Kyzylkum defeated Dynamo 2-0, Mashal outclassed Navbahor 3-1 and Khorezm were held 0-0 by Nasaf.
STANDINGS: 1. Bunyodkor 54, 2. Pakhtakor 39, 3. Nasaf 31, 4. Neftchi 29, 5. Almalyk 29.