Pedro Neto found the net and Reece James banked another hour of game time as the Chelsea duo stepped up their preparations for this summer's World Cup on Wednesday night.
Neto started the contest with Nigeria at the Estadio Dr. Magalhaes Pessoa in Portugal and provided the breakthrough moment midway through the first half.
After a long pass forward was gathered by Diogo Dalot close to the byline, the Manchester United full-back pulled it back to Neto, whose first touch gave him the space to arrow a low shot into the far bottom corner from 12 yards.
Neto's game time was limited to 45 minutes as the winger was one of nine changes at the break, with former Blues forward Joao Felix replacing him.
Akor Adams had levelled for Nigeria shortly before half-time with another well-taken finish but Portugal secured victory thanks to the goal of the game by Francisco Conceicao, who cut inside on to his left foot and curled a shot into the far bottom corner.
Neto and Portugal will now turn their attention to their first World Cup fixture against Congo DR on Wednesday.
England's game was meant to kick off 15 minutes after Portugal's but a thunderstorm saw the Three Lions' match with Costa Rica delayed by a further hour.
James started at right-back for Thomas Tuchel's side and it didn't take England long to take the lead, as good work from Anthony Gordon on the left flank ended with Declan Rice firing into the bottom corner from eight yards out, with the help of a deflection.
Former Chelsea winger Noni Madueke missed from close range after rounding the goalkeeper and there was a penalty award overturned following a VAR check before half-time, as the Three Lions had to settle for a one-goal lead at the interval.
Costa Rica managed just one touch in England's penalty area and one shot at goal during the the time James was on the pitch before the defender was replaced by Djed Spence as one of six substitutions made just after the hour mark.
Minutes later, a jinking run from Jude Bellingham created a chance for Eberechi Eze and when his shot was blocked by the arm of the Costa Rica defender, Gordon - in the absence of recently-replaced Harry Kane - stepped up to emphatically smash his spot kick into the top corner.
And the victory was rounded off in the final minutes when Morgan Rogers' shot was parried out and Ollie Watkins reacted quickly to nod in from close range to make it 3-0.
England will also kick off their World Cup campaign on Wednesday, when they face Croatia at Dallas Stadium.