The 37-year-old started from the bench in Tuesday's last-16 meeting as the Euro 2016 winners eased to a 6-1 victory.
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Ronaldo's replacement Goncalo Ramos fired in the first hat-trick of the World Cup as Portugal set up a quarter-final tie against Morocco.
But despite the whopping win, the biggest talking point has been Ronaldo's omission from the line-up, which his sister has described as 'humiliating'.
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Santos has been quick to play down a rift in his relationship with Ronaldo, despite the 65-year-old hitting out at the ex-Manchester United striker following his reaction to being substituted against South Korea last week.
He told reporters: "I have a very close relationship. 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."
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Confirming his decision had been tactical not disciplinary, Santos remarked: "This is something that is finished and solved.
"It is also important to look at the example of this player's history, he is one of the best players in the world."
Explaining his reasoning as to why Ramos was preferred instead, Santos stated: "We wanted a team that played with a lot of fluidity.
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"Cristiano is more fixed, he stays in a more determined role towards the box.
"Goncalo has different characteristics: he is very dynamic and that's what he ended up showing us."
Pressed on whether the Real Madrid legend would feature against Morocco, Santos replied: "Ronaldo will definitely (be involved), all the players on the bench can be used.
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"If they are not in the starting line-up they can play later.
"It is important to look at the example of this player's history.
"He is one of the best players in the world at playing professionally, being captain - all we have to do is think about this team collectively."