After Ivan Rakitic gave Barcelona the lead at the Santiago Bernabeu on Saturday, Ramos and Messi collided at the end of the first half.
As the Madrid captain lifted the ball past the Barca skipper, Ramos appeared to push his forearm into Messi's face.
Neither the on-field referee or VAR officials were interested in punishing Ramos for the incident but former Madrid head coach Jose Mourinho made his feelings plain in an appearance as a television pundit.
"I think Sergio Ramos' action probably is coming from a player that knows the game has to change," Mourinho said on beIN SPORTS.
"And probably he does it with the intention of creating a different temperature for the second half, because the game until then was really soft, in my opinion."
Ramos, no stranger to disciplinary controversy, denied he had set out to hurt Messi, however.
"I didn't mean to catch Messi, but he took it badly," Ramos told Movistar, with the result coming at the end of a week in which Madrid lost 3-0 to their rivals in the Copa del Rey.
"It's a shame that we're gone [from the title race] and the distance is so big, but we're going to keep fighting because everything is possible. We congratulate them on the result. We played well but it was not enough.
"It has been two very intense matches, with a very high level of effort, it is obvious, we have not had much time to recover, they do not either, so it is not an excuse for us."
Madrid goalkeeper Thibaut Courtois had little to do but he was given no chance by Rakitic's excellent finish.
And the Belgium international feels Madrid's lack of goal threat, having failed to score in either Clasico this week, proved costly.
"I think we played well," he told Movistar. "Barca had more chances and they scored. To win the game you have to do that.
"I would not say [the lack of goals] is a problem. Sometimes we were just missing the final ball and there were also two blocks from [Clement] Lenglet.
"We played well in both games. The only thing is that we didn't score. If you do not score, you lose."