Lille centre-back Fonte, 36, who made the last of his 42 international appearances in November las year, has been replaced in Fernando Santos's squad by Granada's uncapped Domingos Dauarte.
"The other players and staff have undergone tests which have negative results so are available to Fernando Santos," the FPF said in statement.
The European champions host their Iberian rivals in Lisbon before heading to France in the Nations League on Sunday and welcoming Sweden on 14 October.