Before kickoff, Atleti fans vandalised Felix's plaque and burned an Atletico shirt with his name over it.
Felix was returning to Atleti as a loan player with Barcelona, where his future remains undecided.
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His name was also greeted with loud jeers when it was announced as part of the line-ups before kickoff.
However, he had the final say as Felix scored and Barca won 3-0 at the Metropolitano.