McClaren’s decision to drop the forward for last weekend’s game against Liverpool surprised many fans.
Perez has been one of the relegation-threatened club’s better performers this season.
But his team selection paid off, with Siem de Jong, handed a his first Premier League start of the season in the game, helping Newcastle to a 2-0 win at St James’s Park.
Head coach McClaren felt United needed de Jong’s “experience” up front alongside Papiss Cisse after back-to-back defeats to Crystal Palace and Leicester City.
Asked about his decision to leave out three-goal Perez, McClaren said: “Ayoze is a fantastic player.
“Sometimes form goes up and down. We’ve got good players.
“I’ve got to say Siem de Jong has been very frustrated, but very patient, and I think he deserved his opportunity after coming on against Crystal Palace.
“We said ‘we’ll just go for a bit of experience with Siem de Jong and Papiss, and they worked well together.”
McClaren must now decide whether to change a winning team for Sunday’s game against Tottenham Hotspur.
Perez, linked with a move to Tottenham, scored in last season’s 2-1 win at White Hart Lane.
And McClaren admits he has a “dilemma” ahead of the fixture.
“It’s always a dilemma,” he said. “I don’t like doing it, as you like to gain momentum, but Tottenham are a different opponent and a different proposition.”