Messi went on to score the winner in a 3-2 win for Barca following Ramos' dismissal, with the defender having exchanged words with fellow Spain international Gerard Pique on his way from the field.
Ramos also applauded as he departed the Santiago Bernabeu pitch, with Madrid's appeal against the dismissal having been rejected by the competition committee of the RFEF, which described the foul on Messi as a "violent act" in its ruling.
Neymar was banned for the Clasico after sarcastically clapping the match officials following his red card in a defeat at Malaga, which earned the Brazilian a two-game extension to his one-match ban.
But Ramos avoided any further punishment for his red card as the referee Alejandro Hernandez Hernandez made no mention of his clash with Pique or the Madrid skipper's applauding on his departure in his report.
Barcelona's Clasico victory sent them top of La Liga via their superior head-to-head record against Madrid, with both teams in league action on Wednesday as Barca host Osasuna and Madrid travel to Deportivo La Coruna.