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The 35-year-old Juventus forward is asymptomatic and will miss Wednesday's UEFA Nations League game (local time) against Sweden as he self-isolates.
The federation added that the rest of the Portugal squad had undergone tests as a result of Ronaldo's positive, but that they had all tested negative and would be available for the Sweden match.
"No team can be better without the best player in the world but this team has already demonstrated that collectively it has the capacity to tackle the situation," Portugal head coach Fernando Santos told a news conference.
"He [Ronaldo] is managing the situation very well. He is in the room, saying he wants to play, he talks to us from upstairs [from his balcony]," Santos jokingly added.
"He is completely asymptomatic, he is okay, without any symptoms, he doesn't even know what happened to him."
Five-times world player of the year Ronaldo appeared in his side's 0-0 draw away to France in the Nations League on Sunday and last week's goalless draw in a friendly at home to Spain.
He will now be doubtful for Juve's Serie A trip to Crotone on Saturday and their Champions League group stage opening game away to Dynamo Kyiv next Tuesday.