"Disciplinary charges have been pressed against the Vojvodina Novi sad club, their staff, officials and players," the FSS said in a statement following Wednesday's final.
"We believe that swift and comprehensive action is the best way to restore order, identify the perpetrators and make sure this doesn't happen again.
Vojvodina, led by coach Zoran Milinkovic, walked off the pitch in the 80th minute to protest against some controversial refereeing decisions, handing Partizan their 12th cup title.
"What happened is a scandal of unseen proportions in the 63-year-old competition and the FSS has the strength as well as the capacity to deal with the problem and the individuals who caused it," the FSS statement added.
Partizan, who are also close to retaining their league title, led 2-1 in the final after midfielder Zvonimir Vukic converted a controversial spot-kick and Vojvodina then had a goal disallowed and a strong penalty claim turned down.
EMBARRASSING ENDING
Having sarcastically applauded referee Slobodan Veselinovic and Partizan's players, who tried to persuade them to carry on, the Vojvodina team headed for the tunnel and boycotted the trophy presentation.
Vojvodina's fans and president Ratko Butorovic, who was watching the match among the club 's diehard fans, also left in a hurry in the most embarrassing ending to a Serbian Cup final.
"We will accept any reasonable decision but we are bracing ourselves for further punishment after having the Cup title ripped away from our grasp," Butrovic had told reporters.
"We will forgive the referee if it turns out he had a bad day but this looks more like malicious intent and a case of double standards."
Partizan's board accused Vojvodina of undermining the Cup final with "unacceptable behaviour" before and during the match and the FSS for allowing it to happen.
"We would like to know why the FSS allowed Vojvodina to delay the kickoff by 25 minutes just because some of their fans were late and how the most coveted game in Serbia's club football got turned into a circus," it said.
"It appears the match started and ended when Vojvodina saw fit and their frivolous behaviour has ridiculed the very essence of the game's rulebook."
League leaders Partizan are on course to win a record fourth successive championship. They are five points ahead of rivals Red Star and eight clear of Vojvodina with four games left.
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