The 35-year-old is “doing well, without symptoms, and in isolation”, the FPF said in a statement.
Portugal faces Sweden in a Nations League group game on Wednesday.
The remainder of Fernando Santos’ Portugal squad has tested negative for Covid-19 and is available for selection.
Portugal played out a 0-0 draw with France in Paris on Sunday and are top of the group, level on points with the world champions.
The Portugal captain became the first European to score 100 international goals in men’s football when his side beat Sweden in the reverse Nations League fixture in September.
As a result of his period of quarantine, Ronaldo is also set to miss Juventus’ Serie A fixture at Crotone on 17 October and his side’s opening Champions League group game against Dynamo Kiev on 20 October.