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 game.
Violent scenes erupted shortly after Connor Wickham scored in the 90th minute to give England a 1-0 win.
The cases will be discussed at the next ordinary hearing of the Uefa Control and Disciplinary Body on 22 November.
A Uefa statement read: "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.
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"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."
Moments after Wickham's strike, which ensured Stuart Pearce's side qualified for Euro 2013, a series of scuffles between players and staff on both sides broke out as missiles were thrown on to the field.
Sunderland's Danny Rose was sent off after the final whistle for kicking the ball away in reaction to the abuse he was receiving. He later claimed the abuse was racial.
However, the Serbian FA released a statement on Wednesday saying a connection between the on-pitch scuffles and racism had "absolutely no ground" and also blamed Rose for the clashes because of "inappropriate, unsportsmanlike and vulgar" behaviour.
The FA rejects that version of the events and urged Uefa to take the "strongest possible action" against anyone found guilty of racism.
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 are making a formal complaint to Uefa today.
"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."
Uefa has charged the Football Associations of England and Serbia in the wake of Tuesday's Under-21 match.