Prior to the kick-off at the Bernabeu, a fan appeared to make the fascist gesture as the television cameras panned to the crowd.
In a statement, Los Blancos said they had asked its disciplinary committee "to initiate an immediate expulsion procedure" for the fan after the gesture was seen.
"Real Madrid condemns this type of gesture and expression that incites violence and hatred in sports and society," it added.
Now, the European governing body has announced that the club will have to pay €15,000 (£13,000/$17,400) for the "racist and/or discriminatory behaviour of its supporters."
Madrid have also been ordered to close 500 seats in the lower south stand during their next home European match, with the punishment suspended for a year.
In an official statement confirming the sanctions, the CEDB noted:
"To fine Real Madrid C.F. €15,000 and to order the partial closure of Real Madrid C.F. stadium (i.e. 500 adjacent seats of the lower south stand), during the next one (1) UEFA club competition match in which Real Madrid C.F. will play as host club, for the racist and/or discriminatory behaviour of its supporters.
“Said stadium closure is suspended during a probationary period of one (1) year, starting from the date of the present decision."
Real beat Benfica 2-1 in the second leg of their knockout round play-off tie to progress 3-1 on aggregate to the last 16 of the Champions League where they will face Manchester City.