Scottish midfielder Fletcher was sent off for a challenge on Arsenal's Cesc Fabregas late in United's semi-final second leg victory last Tuesday.
European soccer's governing body initially said the only grounds for appeal were in a case of mistaken identity but United, encouraged by comments from UEFA general secretary David Taylor, appealed on compassionate grounds.
Barcelona's Abidal was sent off for what the referee saw as a trip on Nicolas Anelka in Wednesday's semi-final second leg against Chelsea, while Alves was booked for a challenge on Ashley Cole.
Barcelona coach Pep Guardiola said last week the club were appealing out of respect for the players.
All three will miss the final in Rome on May 27.
UEFA, announcing the decision of its Control and Disciplinary Body on Monday, said in a statement that the two clubs had failed to get their appeals in on time, but even if they had made the deadline they would have been rejected.
"There were no grounds for contesting the referees' original decisions," the statement said.
