Igor Jelich found back of the net with an amazing long-range shot in the 19th minute of the game at the Lokomotiv Stadium.
In 37 minutes, the referee Riskullaev pointed to the spot after Marat Bikmaev was fouled in the box and the 32-year-old converted a goal without a mistake.
Dragan Ceran halved the deficit with his 50-minute goal from a close range, but Marat Bikmaev easily scored his second in the 69th minute of the game.
A 87-minute strike from Tiago Bezerra gave hopes for FC Pakhtakor in injury minutes, however, the score remained unchanged at the full time.
Superleague Matchday 31