The defender and midfielder had missed Fernando Santos' men's 2-0 victory over Wales, through injury and suspension respectively.
Pepe, however, was passed fit for the clash and takes up his place in the centre of defence at the expense of Bruno Alves, while Carvalho returns to the first XI in place of Danilo Pereira.
Samuel Umtiti, meanwhile, is rewarded for a fine debut performance against Germany and starts once again in defence for Didier Deschamps' team.
The coach has kept faith with the line-up that downed Germany, with Dimitri Payet, Antoine Griezmann and Moussa Sissoko supporting lone striker Olivier Giroud.
Portugal: Rui Patricio; Soares, Pepe, Fonte, Guerreiro; Mario, Carvalho, Silva; Sanches; Nani, Ronaldo.
France: Lloris; Sagna, Koscielny, Umtiti, Evra; Pogba, Matuidi; Sissoko, Griezmann, Payet; Giroud.