The February 17th defeat to Madrid was marred by alleged racial abuse aimed at the Spanish club's Vinicius Junior by Benfica's Gianluca Prestianni.
Vinicius scored the winner before the alleged abuse led to the game being stopped for around 10 minutes.
Madrid reached the last 16 with a 3-1 aggregate success over the Portuguese outfit on Wednesday.
"Benfica informs they have suspended five members and cancelled their red passes following the initiation of disciplinary proceedings which may lead to the maximum sanction provided in the statutes, expulsion," they said.
"Benfica reaffirm it does not tolerate any form of discrimination or racism and will continue to act firmly whenever behaviours that undermine the values of the club, sport and society are involved," the two-time European Cup winners added.