After the Canarinho went behind, the Barcelona forward set up the equalizer before scoring a stunning solo effort to put his side on its way to a comfortable victory.
The former Santos man scored once and provided an assist, while also having a hand in Brazil's third goal, as the upcoming World Cup host recovered from a shock early concession.
Raul Meireles, who had hit the woodwork six minutes earlier with a header, put Portugal in front in the 18th minute at after making the most of a defensive howler from Maicon.
The Roma right back was attempting to send the ball back to his goalkeeper Julio Cesar via his head, but Fenerbahce midfielder Meireles was quick to realize the opportunity - with the former Chelsea man intercepting with a touch, before tucking away the opener past the helpless Brazilian 'keeper.
But Neymar came to the rescue, putting in the corner that found the forehead of Thiago Silva, before dribbling into the box and tucking away into the left corner of the net to put the South Americans in front at halftime.
Just four minutes after the break, Neymar put through left back Maxwell, who crossed for Jo, who in turn scored his third goal of the week after a brace against Australia.
It was very crisp passing from the Brazilians, who were putting on a clinic for the American fans, and Jo was handed another international goal on a platter after Portugal goalkeeper Rui Patricio was drawn off his line.
Meanwhile, all of Portugal's chances were being blown by winger Nani, who struck two free kicks well over the crossbar, and had another two audacious shots from range that were not close to bothering Cesar.
The result saw Brazil stay unbeaten in its past three clashes with Portugal, winning the two friendlies, while the other result was a 0-0 draw at the 2010 World Cup.