Atletico were awarded a spot kick in the 58th minute of the last 16 first leg clash on Wednesday as Raul Garcia went down in the area under a challenge from Real vice-captain Ramos.
Garcia promptly stepped up and put Atletico ahead, before Jose Gimenez doubled the lead 14 minutes from time.
The defeat leaves Real with a mountain to climb in the return fixture at the Santiago Bernabeu next Thursday.
And Ramos was quick to criticise referee Carlos Clos Gomez, although he is confident Real can learn from the setback.
He told Real's official website: "We are going to try and turn things around in the second leg because this institution and our badge demands that of us.
"Following this defeat we must now focus on Saturday's La Liga match [with Espanyol] and be aware that there is still a second leg to play.
"In my opinion the penalty decision wasn't a foul. It is easy to talk about the referee when you lose and with that in mind I won't go on about it.
"Bad things can also happen in football. Perhaps it is good this has happened to us now and not later on. It will help us to continue improving and that is what we will do."
