Filipe Ramos completely rotated the team after the 2-0 win over Turkey, but Portugal dominated the Welsh side and created several chances to open the scoring earlier.
Cristiano Ronaldo Jr. (42') scored the only goal of the first half with a first-time right-footed shot that hit the post after a good assist from Carlos Moita.
The Al Nassr winger lost the ball several times on the left, but came off in the 62nd minute as the decisive player after a hard-working match, particularly in the first half.
With CR7's son no longer on the pitch, Portugal sealed the win with a brace from Rafael Cabral (65' and 90+1'), who is the Portuguese team's top scorer in the competition with three goals.
The Portuguese team have their final match of the competition on 4 November in Antalya against England at 09:00 Lisbon time.