The Spain international was dismissed in the 77th minute for a two-footed tackle on Messi in midfield, with referee Alejandro Hernandez showing no hesitation to pull out a straight red card in the top-of-the-table La Liga clash.
Ramos, however, believes the red card was a harsh decision as he had no bad intentions at the Santiago Bernabeu.
"The red card was excessive," Ramos told reporters.
"I was not going to harm anyone. In my opinion, that was a yellow card, not a red. I was too late, but there was no contact.
"I never have the intention to hurt anyone."
Ramos immediately confronted Hernandez to protest his dismissal and was seen sarcastically applauding as he left the pitch.
Nevertheless, the Madrid centre-back is adamant his gesture was aimed at Barcelona defender Gerard Pique rather than at the referee.
"I did not applaud the referee when I walked off. I was talking to Pique, not to the referee," he added.
"Referees can be right and sometimes they are wrong. This one was decisive. But I was chatting to Pique, not the referee.
"They [Barcelona] have a different understanding of the game and always talk about referees. But we will not talk about referees, that is not our style. Pique always talks about referees. Maybe it is better to talk about the referee sometimes than to keep quiet, but I will not start any controversy.
"I have no problem with Pique, but he might not get a hug after a Clasico like this."