The defender lambasted Clasico match official Alberto Undiano for turning down what his side thought was a stonewall spot kick appeal in the second period
The Portuguese attacker went down under Javier Mascherano's challenge in the Catalans' area as Los Blancos sought an equalizer, having fallen behind to Neymar's first-half strike.
But referee Alberto Undiano's waved away Madrid's protests, much to the disgust of Ramos, who felt the match official had effectively decided the game in the hosts' favor.
"We have been harmed, the penalty was so clear," the 27-year-old said to reporters after the match. "There are things that we can't fight against.
"The referee was determinant. Real Madrid played well against a hard team. It's been a long time since we saw Barcelona suffering and wasting time."
Shortly after the incident, Alexis Sanchez doubled the hosts' advantage, though Jese Rodriguez netted a consolation in stoppage time.
Carlo Ancelotti's men now find themselves six points off the pace at the top of La Liga.