The Red Devils conceded twice in 20 minutes which prompted Amorim to replace the Dutchman with Kobbie Mainoo well before halftime in the 33rd minute.
Speaking to Sky Sports after the game, Amorim explained why he made the change and how hard it was to remove him from the game knowing it would have a major impact on his already crumbling confidence.
"I talked with Josh about that, because it's important to express the message, but I'm always thinking about the team, and, in that moment, it was important for the team (for) Josh (to) go out.
"You have to think about the team and also, sometimes about the player, because the player is suffering. I was there a few years ago and I know that he wants (it), because I saw it during the week, and that's the most important thing."
"I felt that the team was suffering another midfielder to have more ball, and then we start to have more ball with Kobbie Mainoo.
"It was really, really, really tough on me to do that (substitution)."
Zirkzee has just 4 goals and 2 assists in 27 appearances for United this season since signing from Bologna in the summer.
"He's a really good lad, so you'll have the support and you will prepare the next game," Amorim added.
"It's some moments, and you have some examples like Harry Maguire, that have some tough moments, but that is life in every profession.
"So we will support Josh and continue because, like I said, Newcastle were a better team. Was not better than Josh, was better than Manchester United."