Pepe, who missed the semi-final against Wales through injury, was passed fit to return in place of Bruno Alves alongside Jose Fonte at the centre of the defence.
William Carvalho, suspended against Wales, was chosen ahead of Danilo as the holding player in midfield.
Cristiano Ronaldo and Nani will lead the Portuguese attack as usual.
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France coach Didier Deschamps named an unchanged team for the third game running with an attacking 4-2-3-1 formation.
Samuel Umtiti will again partner Laurent Koscielny at the heart of the defence instead of Adil Rami with Blaise Matuidi and Paul Pogba playing in front of the back four.
(Reporting by Brian Homewood, editing by Ed Osmond)
