Both sides had chances in the opening half-hour, but it was Bruma who broke the deadlock in the 30th minute for Portugal, before Aladje doubled the lead four minutes later, tapping in the rebound from a Samuel Okani save.
The Super Eagles made a bright start to the second half, testing Jose Sa twice within 10 minutes of the restart.
Nigeria's attacking style paid off when Abduljaleel Ajagun fired the ball in, getting his team back into the game, before adding his second in the 67th minute to level the scores.
However, the Portuguese reclaimed the lead less than two minutes later, with Bruma finishing from a Ricardo Esgaio delivery.
Nigeria fought hard as they looked for another equaliser, but Sa remained sharp between the posts to keep their efforts out, securing a win for Portugal.