The Montenegrin representative was defeated by the Finnish Old Power 14:4 in the semi-final match tonight in Niš.
He lost to the same rival yesterday in the group stage of the competition.
Nikšić won 11:4 against Finnish Aisti Sport in the quarter-final match earlier today.
The rival of coach Nikola Čurović's team in Sunday's match for third place and a place in the final tournament will be Cankaja, which was convincingly defeated by Nilufer 13:4 in the Turkish derby.
That duel is scheduled for tomorrow at 9:50 a.m.
The final match will start at 11 am.
The best three teams from Niš will qualify for the Champions League final tournament, which will be played in Berlin from September 16th to 20th.
The Swedish Gothenburg, the British Fen Tigers, the Portuguese Atletico e Cultural, the Danish Aarhus, the Polish Krakow and the Hansa from Rostock qualified for the season finale in Berlin, from the Portuguese tournaments in Odivelas and Barcelona.