On Wednesday, the 33-year-old denied an allegation that he raped Kathryn Mayorga in 2009 in Las Vegas but his omission comes somewhat as a surprise.
Ronaldo said he was calm over "any and all investigations" as he had a "clear" conscience over the allegation.
The Portugal captain who joined Juventus for £99.2m in July, has scored 85 goals in 154 games for his country and won Euro 2016.
Despite the absence of the 33-year-old, Santos reaffirmed he will remain an integral part of the national team's plans going forward.
"In the future, nothing prevents Cristiano from giving his contribution to the national team," he said, as quoted by the European champions official Twitter account.
Portugal squad in full: