Ferguson's assistant Mike Phelan was sent instead, and told assembled media his boss was "distraught" after Man United's 2-1 loss on Tuesday, when Madrid came back from a goal down after winger Nani was given a disputed red card. Madrid won 3-2 on aggregate to advance to the quarterfinals.
UEFA said its disciplinary panel will judge the case on March 21. Ferguson is likely to be ordered to pay a small fine.
Champions League regulations compel clubs to "make their manager/head coach available" for a UEFA-run news conference within 20 minutes of the final whistle.
United players also snubbed post-match interviews, despite clubs being required to "use their best efforts" to provide players for interviews within 15 minutes after the match if a UEFA media official requested them.
UEFA said the panel will also consider extending an automatic one-match ban which Nani must serve. All players receiving red cards for serious foul play in a UEFA match have their case referred to the disciplinary body.
United led 1-0 when the Portuguese winger was sent off by Turkish referee Cuneyt Cakir for leaving his right boot dangerously high when trying to control a ball, inadvertently planting it in the chest of Madrid defender Alvaro Arbeloa.
That red card infuriated Ferguson, who remonstrated with the fourth official on the touchline after the 56th-minute incident. Within 15 minutes, Madrid had scored twice to lead for the first time in the two-legged tie.
"We had a very distraught dressing room and a very distraught manager — and that's why I'm sat here in front of you now," Phelan said at the news conference.
UEFA did not open disciplinary proceedings relating to United players angrily confronting the Turkish referee after the match.