The 18-year-old Manchester United supporter was watching at home in a village near Bingham, Nottinghamshire.
He felt the red card shown to the United winger was a crime so called police.
He later apologised for the call, saying he was caught up in the moment. Police will not take any action.
The fan, who has not been named, called police at about 21:20 GMT during United's second leg clash against the Spanish giants.
He was incensed by the referee's decision to show Nani the red card for a high challenge on Alvaro Arbeloa.
Ch Insp Ted Antill said: "While this recent example may be amusing, it illustrates the sort of insincere calls we have to deal with on a daily basis in the control room.
"They waste our time and they direct us away from genuine victims of crime, particularly if we dispatch officers out to something that turns out to be a bogus report."
He warned that prank 999 calls were a crime and said people had been prosecuted in the past.
"It's no joke. In this case, the man realised his bad judgement and apologised and we decided not to pursue it further," he added.
Nottinghamshire Police said it received 6,933 recorded hoax calls in 2012, which is about 2% of all reported incidents.
Had Tuesday's 999 caller followed Sir Alex Ferguson's example, he would have avoided a police telling off - the Manchester United manager was said afterwards to be "too distraught" to speak about the match.
The game turned after the dismissal of Portuguese winger Nani - whose real name is Luis Carlos Almeida da Cunha - with Real Madrid scoring two quick goals to win the match 2-1, knocking United out of the competition 3-2 on aggregate.
A football fan was so disgusted with the referee's decision to send off Nani in Tuesday's Champions League clash with Real Madrid he called 999.