Ronaldo, 33, last played for his nation at the World Cup in Russia, where the Portuguese were eliminated by Uruguay in the round of 16, FourFourTwo reported.
Without him, Portugal has managed to reach the Nations League Finals, becoming the first side to qualify after Saturday's 0-0 draw with Italy in Milan.
But Santos said there should be no questions that the Juventus star is still an important part of his squad.
"There is no doubt. If you still have doubts, I don't know," he told a news conference.
"But Cristiano Ronaldo is part of this team."
Ronaldo is Portugal's all-time leader in both goals (85) and appearances (154), while only Iran's Ali Daei (109) has netted more times in internationals.
Santos was left satisfied following a goalless draw with Italy.
While not particularly happy with Portugal's performance, Santos was glad to secure top spot in Group 3.
"I am satisfied. To be present in the final phase of this competition is always important for Portugal, shows the quality of Portuguese football," he said.
"It's fair, in a very difficult game, with much more suffering than I expected.
"The first half was very difficult, we had a lot of difficulty adapting, mainly to the defensive actions.
"To defend well isn't to have many players behind the ball, it is to manoeuvre the opponent and not allow them to play.
"When you don't do this, you have difficulty playing too. We were poorly positioned defensively and when we won the ball, we couldn't play."
Portugal are unbeaten in the group ahead of hosting Poland, which is relegated, on Tuesday.
Roberto Mancini credited Italy for taking "a step forward" in Saturday's game but rued the team's profligacy.
The Azzurri were dominant for most of the match at San Siro, creating particularly good chances in the first half.
Ciro Immobile was especially culpable, firing over from close range early on and then shooting at Rui Patricio in a one-on-one situation just after the half-hour mark.
"What matters most in football is scoring goals. We must improve in terms of taking our chances," Mancini told reporters.
"We dominated Portugal and then the decline in the second half was due to us getting tired physically. That was only to be expected, as we cannot play in their half for the full 90 minutes.
"But it is a step forward compared to the Poland game [a 1-0 win last time out in the Nations League], as Portugal is superior to Poland and we controlled the game throughout.
"We tried to play for a result and also give valuable experience to the younger players."
Giorgio Chiellini, who made his 100th Italy appearance, echoed the sentiments of his coach, though he is convinced their problems in front of goal will solve themselves in due course.
"We have the foundations," he added. "We dominated the European champions, and the issue of not scoring goals will improve in time.
"We are still getting to know each other. There is another friendly [against United States in Genk] on Tuesday, and from March the three points start to really count [in Euro 2020 qualifying], although I think we did the Nations League justice and played for the result."