Despite the controversial call, the Turkish referee may just have passed a UEFA audition to be selected for the final in May.
With United leading 1-0 on Tuesday, Cakir red-carded Nani in the 56th minute after the United player stretched his leg to try to control the ball but caught Alvaro Arbeloa in the chest with the studs of his right boot.
Madrid then scored two quick goals and won 2-1, advancing to the quarterfinals 3-2 on aggregate.
Cakir was watched at Old Trafford by UEFA head of referees Pierluigi Collina, who has overseen the 36-year-old official's rapid rise, including nomination to FIFA's shortlist for the 2014 World Cup.
UEFA declined comment Wednesday, which is the European body's usual response to questions about their referees.
After promoting Cakir to its top-tier status in 2011, UEFA has consistently given him big assignments and proposed him for FIFA competitions. He has shown no fear of sending off players whose reputations did not shield them from the letter of football law.
Before Nani, Cakir showed red cards this season to England captain Steven Gerrard in a World Cup qualifier, Barcelona midfielder Sergio Busquets in a Champions League match and Chelsea defender Gary Cahill in the Club World Cup final.
When UEFA backed its referee's judgment by banning Busquets for two Champions League matches after his robust challenge on Benfica defender Maxi Pereira, the Catalan club's appeal was dismissed.
Cakir appears to have judged that Busquets, Cahill and now Nani used "excessive force," which the laws of football say must lead to a red card. The guidelines to "Law 12 - Fouls and Misconduct" defines excessive as when "the player has far exceeded the necessary use of force and is in danger of injuring his opponent."
Had Cakir, from his angle, seen Nani act in a "reckless manner" — "with complete disregard to the danger to, or consequences for, his opponent" — then a yellow card would be enough punishment.
"Not in a million years would we see a Red Card for that in The Premier League but on the continent it's a definite Red," Michael Owen, the former Man United and Madrid forward, wrote on Twitter. "Can't really blame the Ref for it as he is obliged to play to the rules but it's a hard one to take bearing in mind there was no intent."
One English county police force said Wednesday that an 18-year-old Man United fan was "so disgusted with the referee's decision" that he called the emergency number to report it as a crime.
English media joined a chorus of criticism Wednesday, branding Cakir "card-happy" for his track record in big matches.
Still, Cakir's biggest decisions — including sending off Chelsea captain John Terry in last season's Champions League semifinals in Barcelona — has boosted his standing with the game's governing bodies.
UEFA gave Cakir three matches at the 2012 European Championship and rewarded him for his handling of a testy Spain semifinal match against Portugal, showing nine yellow cards. He was the fourth official for the final.
Collina was involved in those decisions and his true opinion of Cakir's performance in Manchester will probably only become apparent when UEFA allocates assignments in the later stages of the Champions League.
For the past two seasons, UEFA gave the honour of refereeing the Champions League final to an official who impressed in the last 16 and then was allowed to skip matches in the quarterfinals and semifinals — Viktor Kassai of Hungary in 2011, Pedro Proenca of Portugal last year.
UEFA will likely choose its referee about one week ahead of the final on May 25 at Wembley Stadium in London, then announce its selection two or three days before the game.