England Under-21 boss Stuart Pearce has said Serbia have been reported to UEFA after his players were racially abused at the end of their Euro 2013 play-off win in Krusevac.
Defender Danny Rose gestured that monkey noises had been made towards him by the crowd before he was sent off after the final whistle.
In further ugly scenes, scuffles broke out when fans entered the field after England had clinched a place at next summer's finals in Israel.
Pearce told ESPN: "I think there were one or two racist incidents that came on from the crowd and they have been reported to UEFA, I believe, by ourselves.
"It is in their hands now, they will have to deal with that. I am very proud of my players and my staff and very proud of the achievement in getting to a fourth tournament in a row."
Steve Wigley, one of England's coaching staff, also appeared to be caught up in the trouble as the players left the field.
Pearce said: "It is very sad, but we are united as a team and a staff. A lot is happening in our country with regard to stamping out racism and I am very proud of the reaction of our players towards the end.
"It is a real shame because over two ties, it was a really close game - two good teams going hammer and tongs at each other. It is just a shame it was soured in the last few minutes of the second leg of the tie."
He added: "Savo Milosevic, their technical director, has come to our dressing room and apologised for any behaviour that was unsavoury. I never want to see any football matches end like that - this is a sporting arena."
In a statement, the FA later added: "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."
Former England captain Paul Ince, working as a pundit on ESPN, felt the visiting players conducted themselves well in the circumstances.
He said: "If you are black, it is hard to actually keep control of yourself because you are the one having the racist chants. From looking at what we have seen on TV, they have done very well to keep cool heads.
"It is a shame because tomorrow we will be talking about something we don't want to talk about. What we should be talking about is England qualifying for Israel in 2013."
Pearce was at least able to draw on the positives of his side's victory.
"The important thing, when the dust settles, is we are going to a championship because we deserved to over two legs," he said. "Our players have put a lot of hard effort and sweat to get there. There is a real collectiveness here. We will let the authorities deal with this.
"All we know is we have given a good account of ourselves over two matches, we have won nine out of 10 matches in qualification and I am very proud of my team."