Sunderland striker Conor Wickham netted an injury-time winner to send England U21 to the 2013 Euros.
Players appeared to be pelted with missiles after Wickham struck in injury time of the second leg to book England's trip to next summer's finals in Israel.
Supporters came onto the field, scuffles broke out and England's Danny Rose was sent off after the final whistle. He reacted angrily by kicking away the ball and appeared to indicate he had been racially abused as he left the pitch.
Steve Wigley, one of the England coaching staff, also appeared to become caught up in the trouble as the players left the field.
The ugly scenes overshadowed another fine display of defensive resilience from England.