It was an unusual move as five-times World Player of the Year Ronaldo, who is his country's most capped player and all-time record scorer, rarely misses even friendlies.
"After talking to the player, and after he moved to Juventus with all the processes of adaptation that entails, we understand it was best for him to not be present for these games," Santos told reporters.
The 33-year-old joined Juventus from Real Madrid in July and has yet to score for his new club in two outings.
Portugal, knocked out in the last 16 of the World Cup by Uruguay, face Croatia in a friendly on Sept. 6 and Italy in their opening Nations League match four days later.
Goalkeeper Anthony Lopes, defenders Ricardo Perreira, Bruno Alves and Jose Fonte, midfielders Joao Mario, Joao Moutinho, Adrien Silva and Manuel Fernandes and forward Ricardo Quaresma were the other World Cup squad members left out.
Goalkeeper Claudio Ramos, defender Pedro Mendes and midfielder Gedson Fernandes were called up for the first time.
Squad:
Goalkeeper: Beto (Goztepe), Claudio Ramos (Tondela), Rui Patricio (Wolverhampton)
Defenders: Cedric Soares (Southampton), Joao Cancelo (Juventus), Luis Neto (Zenit St Petersburg), Mario Rui (Napoli), Pedro Mendes (Montpellier), Pepe (Besiktas), Raphael Guerreiro (Dortmund), Ruben Dias (Benfica)
Midfielders: Bruno Fernandes (Sporting), Gedson Fernandes (Benfica), Pizzi (Benfica), Renato Sanches (Bayern Munich), Ruben Neves (Wolverhampton), Sergio Oliveira (Porto), William Carvalho (Betis)
Forwards:- Andre Silva (Sevilla), Bernardo Silva (Manchester City), Bruma (RB Leipzig), Gelson Martins (Atletico Madrid), Goncalo Guedes (Valencia), Rony Lopes (Monaco)
(Writing by Brian Homewood; Editing by Toby Davis)
