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.
UEFA said in a statement: "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."
It went on: "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."
Danny 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 play-off second-leg win which saw them qualify for Euro 2013.
The England defender said he had been subjected to monkey taunts long before the violent and chaotic ending.
The Serbian FA have denied there were any racist chants before and during the match.
- Football Association of Serbia