Rose had earlier called for Serbia to be banned after complaining of racial abuse and being hit by missiles during his side's 1-0 win on Tuesday.
The England defender said he had been subjected to monkey taunts long before the violent and chaotic scenes which marred the end of the Euro 2013 play-off.
In a statement on its website, the Serbian FA said: "(The) FA of Serbia absolutely refuses (sic) and denies that there were any occurrences of racism before and during the match at the stadium in Krusevac."
The statement continued: "Making connection between the seen incident - a fight between members of the two teams - and racism has absolutely no ground and we consider it to be a total malevolence.
"Unfortunately, after the fourth minute of the additional time and the victory goal scored by the guest team, unpleasant scenes were seen on the pitch.
"And while most of the English team players celebrated the score, their player number three, Danny Rose, behaved in inappropriate, unsportsmanlike and vulgar manner towards the supporters on the stands at the stadium in Krusevac, and for that he was shown a red card."
The Balkan nation's government, however, condemned the racist chants of the home fans, which were clearly audible on video footage from the match.
"I firmly condemn the provocation and insults against the English players in the strongest terms," Serbia's minister of sport Alisa Maric said, putting her government on a collision course with an FA that is deeply unpopular among many Serbians.
"I completely oppose all forms of violence and discrimination, particularly at sporting events and urge the FSS to follow the law of the land, which strictly stands against violence and its manifestation in sport."
UEFA has since opened disciplinary proceedings against both the FA and their Serbian counterparts.
The Serbian FA has been charged with alleged racist chanting by fans, and both associations over the behaviour of players at the end of the stormy encounter which saw violent scenes after the final whistle.
"These cases will be discussed on the occasion of the next ordinary hearing of the UEFA Control & Disciplinary Body on 22 November 2012," it stated.
Serbia have been in trouble repeatedly for fan violence and racism and were threatened with expulsion by UEFA chief Michel Platini following a riot in Genoa that led to the cancellation of a Euro 2012 qualifying match against Italy.