The decision comes after head coach Jorge Jesus denied reports of a rift with the Portugal captain, following claims that Ronaldo had refused to train with the squad.
Ronaldo had previously considered retiring from international football after the World Cup but decided to continue playing as he pursues the milestone of 1,000 career goals.
The 41-year-old Al-Nassr forward was included in Jesus' 25-man squad for the current international break and started Portugal's opening Nations League match against Wales.
However, Ronaldo was left on the bench during Portugal's 2-1 victory over Norway in Oslo on Sunday. He did not join his teammates in acknowledging the visiting supporters after the final whistle, instead heading straight to the dressing room.
His actions led to speculation that he was unhappy with Jesus.
Speaking before Portugal's Nations League meeting with Denmark on Thursday, Jesus rejected suggestions that there had been an incident involving Ronaldo.
"There was no incident whatsoever," Jesus said, explaining that Ronaldo had been informed before the match that he would not start but could be introduced later.
Jesus said he ultimately decided not to bring Ronaldo onto the pitch.
He also dismissed reports that Ronaldo had refused to train on Tuesday. According to the manager, the forward had completed individual exercises focused on mobility and strengthening and was expected to return to normal training the following day.
However, Ronaldo did not join his teammates on the pitch in Denmark. Portuguese media later published footage appearing to show him leaving Parken Stadium alongside two members of the coaching staff.
Ronaldo subsequently confirmed his departure from the national team camp in a post on Instagram.
"After the press conference of the national team and following a conversation with the president of the Portuguese Football Federation, I have decided to leave the national team training camp," he wrote.
He added that he would eventually explain the reasons behind his decision and wished his teammates well in their upcoming matches.
Goncalo Ramos scored Portugal's winning goal against Norway and Jesus had indicated that the AC Milan striker would again start ahead of Ronaldo against Denmark.
"If I need Ronaldo, he'll come on. If I don't need him, he won't," Jesus said.
