Benfica, said in a statement on Monday they "regret being deprived of the player while the case is still under investigation and will appeal UEFA's decision".
Prestianni was seen holding his shirt over his mouth during a heated exchange after Vini Jr scored the opening goal.
The Brazilian told referee Francois Letexier that he had been racially abused, and the game was stopped for 10 minutes due to anti-racism protocols before he and his team-mates temporarily left the pitch.
Prestianni had denied making a racist slur, claiming the Madrid player "misinterpreted what he thought he heard".
Now, he has been banned for one game meaning he will miss the second leg of the Madrid tie with UEFA saying:
“Following the appointment of a UEFA Ethics and Disciplinary Inspector (EDI) to investigate allegations of discriminatory behaviour ... and upon request of the EDI with an interim report, the UEFA Control, Ethics and Disciplinary Body (CEDB) today decided to provisionally suspend Mr Gianluca Prestianni for the next UEFA club competition match.
“This is without prejudice to any ruling that the UEFA disciplinary bodies may subsequently make following the conclusion of the ongoing investigation and its respective submission to the UEFA disciplinary bodies. Further information about this matter will be made available in due course.”
Vinícius did not speak after the match but posted a message on Instagram that said: “Racists are above all cowards (who) need to put their shirts over their mouth to demonstrate how weak they are.”
Benfica boss Jose Mourinho has meanwhile cancelled his pre-match press conference ahead of the meeting in Madrid as the club deal with the situation.