Ronaldo, who was substituted early on in the contest due to a knee injury, was later seen manically gesturing to his teammates from the sidelines.
A Seleção eventually triumphed thanks to a late Eder strike, but Ronaldo's antics from the dugout courted criticism from the likes of former Portugal star Antonio Simoes.
Asked for his opinion on the matter, Mourinho told Sport TV: "There were 11 players on the pitch doing their job, and the person in charge of them was the coach. I looked at it as an overload of emotion."
He added of his compatriot: "He lost a little emotional control, although that's not a bad thing. I think the 11 who were there in those four or five minutes were totally focused on what they were doing, they had full control of the situation.
"But my experience has told me that, in these moments, when important decisions might need to be made, the players are lost in their own little worlds."
Ronaldo did not always enjoy a smooth relationship with the 53-year-old Mourinho during the three seasons they spent together at Real Madrid.