Aleksandr Kasyan gave an early lead for the hosts converting a goal from a 12-yard penalty spot in the 23rd minute.
However, Sardor Sobirkhujaev and Doston Khamdamov scored two goals in a span of 60 seconds as FC Pakhtakor went to the dressing room with an advantage in the break.
A 67-minute strike from Dragan Ceran ensured Shota Arveladze's side to finish a comeback win claiming three points to have one point adrift of FC AGMK on the top of League table.
Superleague Matchday 7
Stadium: Pakhtakor stadium
Referee: Elyor Tursunov