Temurkhuja Abdukholikov broke the deadlock with his opener from a penalty kick after a 56-minute goalless period.
Ariagner Smit Medina doubled the lead for the Railwaymen in the second-period stoppage time.
Superleague Matchday 15
Stadium: "Lokomotiv" stadium, 1710 spectators
Referee: Akobirkhuja Shukrullaev