Bobir Abdukholikov fired home in the 21st minute of the game as he opened the scoring for the Dragons at the Pakhtakor Stadium.
Dragan Ceran’s header put the sides in level term before FC Pakhtakor took the lead through Jaloliddin Masharipov just 6 minutes later.
Shota Arveladze’s side will face the reigning champions FC AGMK in the final match.
Uzbekistan Cup 1/2 final
Stadium: Pakhtakor stadium
Referee: Temur Tukhtasinov