Speaking on Friday, Santos gave a detailed account of a conversation with Ronaldo during which he told the 37-year-old he would be dropped for the round-of-16 tie against Switzerland.
He also clarified suggestions that Ronaldo had tried to leave the World Cup but afterwards tried to put a stop to questions about the former Manchester United forward.
"I spoke to him after lunch on the day of the game and invited him into my office," Santos said.
"For obvious reasons, Cristiano was not happy about it, as he has always been the starting player.
"He told me: 'Do you really think it's a good idea?' But we had a normal conversation in which I explained my viewpoints and of course he accepted them. We had a frank and normal conversation.
"He has never told me he wanted to leave the national team, and it's high time we stopped with the conversation.
"He decided to warm up with his colleagues and celebrated all the goals we scored. At the end, he was the one who invited his colleagues to thank the fans.
"It's high time to leave Cristiano Ronaldo alone. In every news conference, 90% of the questions are about Cristiano Ronaldo."
In Ronaldo's absence, Portugal beat Switzerland 6-1, with replacement striker Goncalo Ramos, 21, scoring a hat trick.
Santos, however, left the door open for Ronaldo to return to the team for the quarterfinal with Morocco on Saturday by insisting it would be a "different game."
"Every player isn't happy when they are on the bench," Santos said.
"It's totally normal, and managers just have to deal with it. Just because a team wins doesn't mean you don't change. Morocco will present us with different things; they are an extremely well organised team with a lot of quality. You think this match will be the same?"
Santos was joined at his news conference by Joao Felix, who hinted that the players are not happy with the media coverage surrounding Ronaldo.
"I would like to leave a message to the Portuguese people and to the press," he said.
"Portugal is in a great competition. We haven't reached the quarterfinals for a long time. We should all be closer together and not try to make the atmosphere worse."
"I've already said I'm focused 100% on the national squad," he added.
"I'm only concerned with giving a good performance to help this team and Portugal and the Portuguese people. Atletico Madrid is something I have to look at when the World Cup ends because I'm 100% focused here."