The 21-year-old is now self-isolating and could be a doubt for Wolves' clash with Villa a week on Saturday.
Trincao returned a positive rapid test upon arrival at Portugal's training camp on Wednesday.
And according to the Portuguese Football Federation, he then took a PCR test that also came back positive.
Trincao had only just been called up as a late replacement for Benfica's Rafa Silva.
Wolves team-mate Nelson Semedo has now joined up with the squad due to Trincao and Borussia Dortmund's Raphael Guerrero, who has a knock, pulling out.
A statement from the Portuguese Football Federation read: "Francisco Trincao left the stage of the national team after having tested positive for Covid-19.
"The Wolverhampton player performed a rapid test (TRAg), upon entering the stage, which was positive.
"Trincao did not participate in the training session that took place this Wednesday, in Cidade do Futebol, and was immediately placed in the care of the FPF Health and Performance Unit.
"The positive diagnosis was later confirmed by an RT-PCR test.
"Fernando Santos has called up Nelson Semedo for the games against Qatar and Luxembourg, scheduled for Saturday and Tuesday at the Estadio Algarve."
Trincao, who joined Wolves from Barcelona in the summer, had been hoping to add to his seven Portugal caps.
Semedo has 22 to his name so far and joins Wolves team-mates Ruben Neves and Joao Moutinho for the matches against Qatar and Luxembourg.