The Europeans who are without captain Cristiano Ronaldo played with swagger and courage in front of their teaming crowd as they outclassed the toothless Eagles.
Nigeria’s Super Eagles fell behind with few minutes into the game when Manchester United duo Bruno Fernandes and Diogo Dalot combined for the opener.
Dalot set up Fernandes to make it 1-0 after just nine minutes at the Jose Alvalade.
Fernandes made it 2-0 from the spot after the referee pointed to the spot after Bright Osayi-Samuel was adjudged to have handled the ball in the box.
The Super Eagles, however, improved in the second half and were handed an opportunity to be back in the game from the penalty spot.
The referee awarded a penalty nine minutes from time but substitute Emmanuel Dennis failed to beat Rui Patricio in goal for the Portuguese.
Portugal then upped their game and got their third and fourth, through Goncalo Ramos and Joao Mario.
The result means Peseiro has lost four of his seven games as Nigeria’s coach. The first three defeats were against Mexico, Ecuador, and Algeria.