Ramos was lucky not to be sent off for a challenge on Luis Suarez, which saw the 31-year-old receive a yellow card for hitting the Uruguay international in the face during the second half.
The Spain international was asked about the incident after the loss, and risked the ire of Barca fans by referring to exiled Puigdemont in his post-match comments.
Puigdemont is currently in exile in Belgium and is viewed as the President of Catalonia by supporters of Catalan independence. However, in October, the 54-year-old fled the country for fear of imprisonment from the Spanish government.
"In Barcelona, sure they think I should go to jail with Puigdemont. I had no intention to hit Luis Suarez," Ramos told reporters.
“A failure not to win the Clasico? Anyone who thinks that just needs to look back at 2017 and review the statistics," he continued.
“The Clasico could’ve been the icing on the cake, but it wasn’t to be. We’ve been hit with the double whammy of the result and falling 14 points behind.
“Still, the league isn’t impossible and we’re obliged to keep fighting. It’s time for us to reflect and keep working."
Madrid now sit fourth in La Liga, 14 points behind leaders Barcelona after 17 games.