Referee Juan Martinez Munuera spotted a shirt pull by the Barca defender on the Real Madrid captain after consulting the pitchside VAR monitor and Ramos converted the penalty, before Luka Modric secured the three points late on.
"There's a referee. He went to look at it and then he gave a penalty," Zidane said when asked about the incident in his post-match news conference. "I never talk about referees, it's a difficult job and I won't start today. He looked at it and blew the whistle and that's all. Independently of that, we deserve our win. It finished 3-1, we could have scored more."
"We had to regain our confidence and this was a good game for that," he said. "I don't know if people have been unfair with the team or with me, but this team has character... We aren't here to shut people up. Our job is to believe in what we do, stick together, and today that's what we did."
Captain Ramos had been an injury doubt, missing the midweek loss with a knee problem, but returned to the side to score his 25th consecutive spot kick.
"Both Lenglet and I mark in a way that goes to the limit sometimes," Ramos said. "It's a penalty for sure, he grabbed me. Judging the referee for that would be unfair.
"It was a week to prove ourselves, and even more so in a Clasico. It's extra motivation. It was a bad week. We couldn't stay on that bad run... Two games are a crisis at Madrid. We have to keep doing our thing and ignore the criticism which tries to destroy the good energy of the group."
The result sees Real Madrid six points clear of Barca in the La Liga table, having played one game more.