The Real Madrid star was forced off in the first half of the 1-0 win over host nation France after sustaining a knee injury in a challenge with Dimitri Payet.
Ronaldo returned to the dugout for extra-time and was seen gesticulating wildly in an effort to encourage his team-mates, at one stage lifting coach Fernando Santos from out of his path.
Former Portugal and Benfica star Antonio Simoes criticised Ronaldo for his antics, and Mourinho has agreed that the 31-year-old’s “overload of emotion” did not help his side’s cause.
“His contribution in the last few minutes of the final was nothing,” the Manchester United boss 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, from someone who saw that the team was just minutes away from achieving the objective that they all wanted.
“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.”
A solitary strike from Eder in extra-time secured Portugal’s first major trophy at the final in Paris.