Garnacho was taken off before halftime as Amorim was forced to adjust his system after Patrick Dorgu's red card.
The Argentina winger chose to go straight to the dressing room rather than take his place on the bench.
United eventually found a way to defeat Ipswich Town 3-2 on the night and Amorim said: "I am going to talk with Garnacho about that.
"The thinking was that we would play 5-3-1. That is a risk because he is the one who can play one-v-one in pace.
"We had to choose someone to go out. It was my choice."
On the home support, the manager also said: "The fans' support was amazing.
"I have felt that since day one.
"They want to see the team fight to the end, no matter what the situation. We did that today. All the things in the game were against us, but we fought through that. You feel the connection. It was a good win for us."