The Cardinals led, 5-3, and there was a runner at second and two outs in the eighth.
St. Louis manager Mike Matheny defended his catcher's actions.
"Yadi was absolutely right," Matheny told reporters after the game. "At some point, somebody's got to say something. 'No more up here.'
"If you're going to miss and you miss in, that's fine. But you can't keep taking shots up there and expect somebody not to say something."
Ramirez was trying to throw inside, but the Cubs said there was no intent to hit Molina.
"There was nothing there," Renteria said. "Both teams should react exactly the way they reacted. That's baseball. You're competing with two division rivals. Was there any intent to try to hit him? Absolutely not. Are the reactions normal? Sure. It's one of your key players.
"You see a pitch that seemingly looks like it's up and in. If you go back to the video, it wasn't as close as you might think. When a pitch is elevated to the mind's eye, it seems like it's very close. I think everybody reacted the way they should when two teams are competing against each other. There's nothing wrong with the way they showed their emotion."
Chicago and St. Louis don't play each other again until July 25 at Wrigley Field.
Carrie Muskat is a reporter for MLB.com. She writes a blog, Muskat Ramblings, and you can follow her on Twitter @CarrieMuskat. This story was not subject to the approval of Major League Baseball or its clubs.