Luis Diaz’s 14th-minute strike gave Porto a shock lead at the Etihad but Sergio Aguero converted from the penalty to spot level things up just six minutes later.
And Ilkay Gundogan and Ferran Torres scored in the second half to win all three points for Manchester City in the first group game of their Champions League campaign.
But Pepe was furious after the game as he felt the home side got a lot of help from bad officiating during the game and insisted that the Citizens are good enough to win games without getting an assist from referees.
The Porto defender insisted that his side should have received a penalty for a foul on him from Joao Cancelo and Rodri should have been sent off following a second bookable offence.
He was furious that despite all the technology available to referees now, in his view they still made basic errors that cost Porto the game.
Pepe was quoted as saying by Portuguese daily A Bola: “The result is completely unfair.
“Manchester City have very good players and did not need this help. So many bad decisions and it cost us even more.
“Today with the technology we have, VAR did not attract the referee’s attention, it is unacceptable.”
He added: “There was a penalty on me, I think it was Cancelo.
“There was also a second yellow that should have been shown to Rodri.”