A Connor Wickham last-minute goal secured the Young Lions' progress to Euro 2013 but the game was marred by clashes between players and staff after the goal, with Danny Rose reacting furiously, and being sent-off, after allegedly being racially abused.
Monkey chants were also clearly audible from the stands with the Sunderland player gesturing towards the crowd as he left the pitch.
An FA statement read: "The FA condemns both the scenes of racism and the confrontation at the final whistle during which time our players and staff were under extreme provocation.
"The FA has reported a number of incidents of racism to Uefa following the fixture.
"These were seemingly aimed at a number of England black players by the crowd. The matter is now with Uefa."
Fists were thrown in scuffles between players and England assistant Steve Wigley was accosted by Serbia's coaching staff as he attempted to run from the pitch, with the Professional Footballers' Association also blasting the unsavoury scenes.
PFA chief executive, Gordon Taylor stated: "The PFA condemns the appalling racist abuse endured by our Under-21 team tonight in Serbia which evoked memories of scenes we all hoped had been consigned to the past.
"We call on Fifa to invoke their full powers to ensure a strong sanction is imposed to send a message that this behaviour is totally unacceptable and that anti-racism is not just a slogan.
"The recent financial punishments handed down to both clubs and national football associations do not send a strong enough message that the football authorities are taking racism seriously.
"Fifa and Uefa need to get tough and deduct points or disqualify teams from competitions."