Perez had another super chance in the 20th minute, but the Spaniard fired over the crossbar from a positive position.
Braga were not without their chances, however, and Wilson Eduardo hit the post in the 26th minute during an open period of the match.
The Portuguese outfit took the lead early in the second period when Ricardo Horta drifted into a dangerous position before curling the ball into the bottom corner of the net.
Horta might have doubled Braga's lead in the 55th minute when he was presented with time and space inside the Newcastle box, but the Portuguese blazed over the crossbar.
The Magpies thought that they had levelled in the 76th minute when Joselu tapped home from close range, but Perez was adjudged to have been offside.
Braga actually doubled their lead less than one minute later, with substitute Joao Novais steering the ball into the bottom corner of the net, before Fransergio headed a third for the home side in the 85th minute.
Braga were not finished, however, and added a fourth through Dyego Sousa in the final minute to cap what was a miserable second half for Benitez's side.
Next up for Newcastle is a clash against Augsburg on Saturday, which will be their final pre-season fixture before opening their 2018-19 Premier League campaign against Tottenham Hotspur on August 11.
BRAGA: Matheus, Sequeira, Wilson (Sousa 81'), Paulinho, R. Horta, Claudemir, Fransergio, Raul Silva, Bruno (Novais 64') Viana, R. Esgaio, M. Goiano
NEWCASTLE: Dubravka (Darloe 73'), Yedlin (Manquillo 73'), Lascelles (Schar 46'), Clark, Dummett, Ritchie (Roberts 80'), Hayden (Ki 66'), Diame, Atsu (Murphy 66'), Perez (Longstaff 80'), Gayle (Joselu 73')