"I have a very close relationship," said Santos. "I know him since he was 19 at Sporting and then he started to develop in the national squad when I arrived in 2014.
"Ronaldo and I never misinterpret the human and personal aspect with that of manager and player. I will always consider that he is a very important player to have in the team."
Portugal produced their most emphatic performance of the World Cup and the 68-year-old boss had to admit he liked the look of his team without their 37-year-old superstar striker.
"That is what was intended, what we wanted," said Santos. "We wanted a team that played with a lot of fluidity. We played very well. We were a team that was circulating, had ball possession.
"We had a lot of trust, played with a lot of determination and unity, and that reflects in the capacity to win back the ball. Everything worked very well."
Santos insisted his decision to leave out Ronaldo had been tactical not disciplinary, after the captain's tantrum on Friday when replaced towards the end of a defeat against South Korea, but the manager soon tired of questions on the subject.
"This is something that is finished and solved," he added. "It is also important to look at the example of this player's history, he is one of the best players in the world."