The Fenerbahce defender found himself free at a late Joao Moutinho set-piece at the Gillette Stadium in Foxborough and headed past a helpless Guillermo Ochoa.
With Cristiano Ronaldo still missing due to injury, Paulo Bento's men had lacked a creative spark until the late winner.
Miguel Herrera started with Manchester United striker Javier Hernandez on the bench, while Rafael Marquez – who had been under an injury cloud – returned to the centre of defence.
Mexico pressed high up the pitch early on, but Portugal created an opportunity in the 14th minute as Vieirinha's strike was kept out by Jose de Jesus Corona.
Eder looked the most likely to score in an uninspiring first half and he had another chance six minutes before the break, only to put Joao Pereira's cross wide.
Bento's men almost took the lead in the 50th minute.
A Nani corner eventually fell to Fabio Coentrao in the area, but the Real Madrid defender's low strike was kept out by substitute goalkeeper Guillermo Ochoa at his near post.
The striker's cross to the back post from the left found the Porto man, who took a neat touch before forcing Eduardo into a strong save from an angle.
Played in behind, Hernandez unselfishly squared for Pulido, but Eduardo was quick off his line to smother at the forward's feet in a one-on-one.
But there was to be late drama as slack marking saw Alves rise in the area to head in Moutinho's free-kick from the right.
