Red Star Belgrade will meet Vojvodina in next month's final after they beat city rivals OFK 1-0 with a late goal in the other semi-final on Wednesday.
Serbian first division top scorer Mrdja, who scored twice in his country's 3-0 World Cup warm-up win against fellow finalists Japan last week, continued his excellent run of form with a pair of headers from crosses by midfielder Dusan Tadic.
Mrdja opened the scoring in the 36th minute from close range after a darting run by Tadic down the right and made it 2-1 in the 49th after Radosav Petrovic had equalised with a searing 20-metre shot on the stroke of halftime.
Winger Mario Djurovski sealed Vojvodina's passage to the final on the hour, rifling an unstoppable shot from 25 metres into the goalkeeper's bottom right corner.
The game was played under tight security following a serious incident during Wednesday's semi-final, when a fan was taken to hospital in critical condition from a gunshot wound sustained during the match.
The 21-year old fan is recovering after having surgery for an abdominal wound he sustained midway through the second half, when he was shot by a still unidentified assailant following a scuffle.
