The Turkish official made the key decision of the tie Tuesday, showing United's Nani a red card for a challenge that ended up with both him and Madrid's Alvaro Arbeloa on the ground.
At that point, United led 1-0 on the night and 2-1 on aggregate, with firm control of the tie and just over half an hour away from a quarterfinal berth.
The decision seemed to swing the contest, with Real suddenly taking the impetus and getting a quick double to send the Old Trafford crowd off booing.
Whether the sending off was justified or not seems to be a hot topic for debate, with some calling it an atrocious decision given Nani's lack of intent while others pointing to the vague laws of the game to justify the referee's decision.
Whether it was a good call or not, though, who is this official who suddenly rose to prominence in this pivotal match in Manchester United's season?
Çakır is a 36-year-old official who began his officiating career in the Turkish Super Lig some 12 years ago.
In 2010, the referee began his Champions League career in a 1-1 draw between Barcelona and Rubin Kazan in a group stage match, with both goals coming from penalties rewarded by Çakır.
Over his past few high-profile assignments, though, the referee's record becomes quite interesting.
Çakır also made the biggest decision of last year's Champions League, sending off John Terry in Chelsea's pivotal second leg with Barcelona at the Camp Nou. In the Club World Cup final with Corinthians, Cüneyt went on to send off Terry's partner in the center of defense, Gary Cahill, as the Blues fell 1-0.
The referee went on to anger all of Ireland, sending off Keith Andrews one minute from time as the Irish fell to Italy at Euro 2012. Finally, Çakır took control of the tournament's epic semifinal between Spain and Portugal, where he booked an incredible nine players.
Finally, in England's 1-1 draw with Ukraine in their 2014 World Cup qualifier at Wembley in September, the Turkish official sent off Steven Gerrard a few minutes before the full-time whistle, adding on to his nine yellow cards.
Obviously, Cüneyt Çakır's decision to show Nani a red card Tuesday was just his latest act of tough law enforcement on the pitch, adding to his curious recent record of decisions that adversely affect British sides.
Such is the Turk's record, in fact, that the great Italian official and most senior member of the UEFA officiating committee, Pierluigi Collina, was sent to Old Trafford Tuesday exclusively to lend support to Çakır in case of emergency.
With all this in mind, United fans will surely be a tad apprehensive next time Cüneyt Çakır is in charge of a match featuring their club.
Then again, perhaps all English sides should share in that apprehension.
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