The Welsh were bidding to be the first British team to reach a Euros final.
Ronaldo headed Portugal ahead after a phenomenal leap, and Nani clinched the victory when he turned home Ronaldo's shot from outside the penalty area.
Wales rarely threatened a comeback despite Gareth Bale forcing two Rui Patricio saves from distance.
Portugal, who have never won a major tournament, face Germany or hosts France in Sunday's Stade de France final.