The two teams will again clash on June 21 at the 2013 FIFA U20 World Cup in Kayseri, Turkey.
Portugal finished second in Group B and will play the third-place play-off against hosts France on Saturday after they finished on seven points and Mexico were pegged to five points courtesy of a 1-1 draw with Belgium also on Thursday.
Portugal scored the first goal through a penalty kick converted by Alves after Nigeria’s goalkeeper Samuel Okani dived on the leg of a Portuguese attacker in the penalty box.
Portugal scored their second goal in the 70th minute when Ricardo Pereira slotted home the second goal after he collected a superb pass inside the Flying Eagles vital area.
The Nigerians got a consolation goal in the 79th minute when Bright Ejike pulled a goal back to keep the final scoreline at 2-1.
Nigeria started brightly but could not have any clear-cut chance at goal.
Portugal Thiago Silva made the first attempt at goal in the 14th minute, when his free kick crashed against the Flying Eagles post.
Okani in goal for Nigeria scrambled for a corner a goal-bound volley from Aladje in the 43rd minute after his misplaced pass gifted Portugal another chance at goal.
Five minutes later, Portugal capitalised on another error from Okani when Ivan Cavaleiro pounced on his spilled ball with a shot which was somehow blocked by Oluwasemilogo Ajayi.
In the 51st minute, a big chance fell to Nigeria but Christian Pyagbara failed to put Nigeria ahead when he had only the keeper to beat as he fired wide.