Perez appeared to react with anger to the decision before having a stern chat with goalkeeping coach and fellow Spaniard Xavi Valero.
But after the match, manager Manuel Pellegrini denied that Perez refused to warm-up by saying: "It is very simple".
However things started badly and they lost their opening four games of the Premier League season, with an EFL Cup win over AFC Wimbledon the only saving grace to the beginning of the season.
Given the false information spread by various media that affect my image, I am forced to explain the only truth: I have never refused to warm up in my career and even less to play. When Marko was injured, I was on the bench after having warmed up.
'The images that have been misinterpreted corresponded to a talk with the goalkeeper's coach, in which I never refused to warm up and explained to what happened.
"It is important for us, I have told the players", Silva said.
'As a professional I accept the decision and will continue working hard to have as many minutes as I can'.
Pellegrini said after the game that he did not use Perez because "Antonio was already ready, so played".
Andriy Yarmolenko put West Ham in command with two goals inside the first 31 minutes on his first Premier League start, with the Ukraine worldwide taking time to settle in England prior to his double at Goodison Park.
The Chilean tactician was celebrating his 65th birthday at Goodison Park, and his players certainly provided him with the ultimate present after clinching three vital points, taking the Hammers off the foot of the table and out of the relegation zone.