UEFA has charged both the Football Association and the Serbian FA following the unpleasant scenes that occurred during and after the Under-21 match between the nations on Tuesday.
England's Under-21 side qualified for next summer's European Championship in Israel thanks to a 1-0 win in Krusevac but the result was marred by alleged racist chanting towards the Young Lions' black players and violence which erupted at the final whistle.
Defender Danny Rose was at the centre of the row, with the on-loan Sunderland youngster claiming he was racially abused throughout the game by Serbian supporters, before being sent off after the final whistle for kicking a ball into the crowd in anger as scuffles broke out.
Rose was pushed in the back as he left the field and gestured to indicate that monkey chants had been aimed at him, though the Serbian FA vehemently denied the allegations of abuse.
However, UEFA has now charged the associations of both countries, with an official statement saying: "UEFA has opened disciplinary proceedings against both the Football Association of Serbia (FSS) and England's Football Association (FA) following a number of incidents during and after England's 1-0 win over Serbia in the 2013 UEFA European Under-21 Championship play-off second leg at the Mladost stadium in Krusevac on Tuesday 16 October 2012.
"Regarding alleged racist chanting, UEFA will instigate proceedings against the FSS over the misconduct of their supporters during and at the end of the match. Proceedings will also be instigated against the FSS for the improper conduct of the Serbia players at the end of the match.
"UEFA will also commence proceedings against the FA for the improper conduct of the England players at the end of the match. These cases will be discussed on the occasion of the next ordinary hearing of the UEFA Control & Disciplinary Body on 22 November 2012.''
In the wake of the statement, the FA has raised the prospect of England's teams boycotting any future fixtures scheduled to be played in Serbia, and has sent a dossier of evidence to UEFA detailing their grievances.
"We were shocked and appalled by the disgraceful events that occurred in Serbia last night," FA general secretary Alex Horne said. "Our players and staff were subjected to racial abuse, violence as well as missiles being thrown at them throughout the match. What occurred is inexcusable and not acceptable.
"We call on UEFA to take the strongest possible action against the Serbian FA, their supporters and anyone found guilty of being involved in the numerous instances of violence and abuse.
"We have also been in contact with UEFA's senior executives to express our deep concern at this matter. It is also clear that we must defend Danny Rose, who was sent off due to the frustration of being a target of racial abuse.
"FA officials made UEFA officials aware of racist abuse from sections of the crowd aimed at a number of England's black players at half-time on Tuesday evening. This matter was discussed again during a meeting with UEFA after those disgraceful scenes which followed the final whistle.
"No football team should be asked to play in any environment where racial abuse, violence and threatening behaviour is prevalent. We must question the validity of sending a team to Serbia in the future.''
Serbia had earlier denied any wrongdoing, with their FA releasing a statement which read: "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.
"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 [an] 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 Serbian FA did, however, issue an apology for the way its players and staff confronted members of the England party, saying: "Football Association of Serbia apologises to the guests from England and the overall football community because of the unsportsmanlike behaviour of a part of the technical staff and players of the Serbian Under-21 team.
"By this we inform the overall public that we will, as a matter of urgency, start an internal disciplinary procedure and punish the culprits after reviewing all the reports. To be honest, we expect the same investigation from the English FA.''
Information from the Press Association has been used in this report