The 23-year-old limped off towards the end of Thursday's 5-0 rout of Gibraltar after hurting his right leg and will sit out the European champions' trip to Basel in their first game in Group B.
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Gomes, who made a switch to the Camp Nuo from Valencia in July, will be replaced in the squad by Porto midfielder Andre Andre, the FPF added.
Portugal were already without captain Cristiano Ronaldo, who continues his recovery from a knee injury sustained in the Euro 2016 final against France.
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