Jovan Jokic opened the scoring in 17th minute of the game from a penalty kick as Almalyk side went to the dressing room with a 1-0 lead at the interval.
After the restart, Esmail Goncalves put the sides on level after the referee showed the point in the 54th minute.
However, FC AGMK returned the lead through Jovan Jokic and Zohir Pirimov, while they claimed the title for the first time in their history.
Ўзбекистон кубоги Финал
Стадион: "Истиқлол" марказий стадиони, 11152 томошабин
Бош ҳакам: Темур Тўхтасинов