Santos was unhappy with the way Ronaldo reacted to being substituted against South Korea and has held clear-the-air talks with him.
Ronaldo was taken off in the 65th minute of Portugal's World Cup defeat by Korea last Friday and there were reports that he swore at Santos.
The pair have now cleared the air ahead of Portugal's last-16 match against Switzerland on Tuesday, with Santos saying the matter is “solved".
“Let me split my answer into two," he said. “The first is when I went to the press conference, as you know, when the match had ended.
“I had a flash interview, you were there, and then obviously I went straight to the press conference and what I said I'll repeat it here again. There on the field, nothing happened, nothing. So I just heard him discussing with the players of Korea, I didn't hear anything else.
“Now the second part of your question, if I have seen the images? Yes. I didn't like it. Not at all. I did not like it. I really didn't like it.
“And therefore from that moment onwards you have people, everything is finished, full stop regarding that issue. Now we have to think about tomorrow's match and everyone is focused on tomorrow's match. The topic is solved. We fix that at home and that's it."
Ronaldo is currently a free agent and has been heavily linked with a move to Saudi Arabia side Al Nassr, with some reports in Spain saying that a deal is now done. Santos insists it has not been a topic of discussion in the Portugal squad and will not distract their World Cup bid.
“I haven't spoken to him about this," he said. “We had a conversation with the players, but I don't really know about this.
“To be honest I didn't know about this. I just heard about this when I arrived here. Someone just told me that a few minutes ago.
“But that's his decision, that's what he has to deal with, and we are totally focused here on the World Cup as a team. That's what we spoke about and that's our focus, and I don't know anything about this other issue."
Santos also refused to confirm if Ronaldo will start against Switzerland tomorrow, saying: “I only decide who is going to be in the team when I reach the stadium. I don't know what the lineup is.
“That's what I have always done and that's what I am always going to do. It's going to be the same tomorrow."