Yamal was forced off with an injury suffered after scoring a penalty on Wednesday night.
The teen is understood to have strained his hamstring and Flick said: "We have to see tomorrow, see what happens. We'll see.
"We have to wait and see what's wrong. He's noticed something, he's had something done to him. He wouldn't leave the field without a reason. We have to accept it. It's not easy, it's a shame for us. Just like Joao. We also have to wait until tomorrow."
The German also said: "He has an injury, but we have to wait to find out how long he'll be out. He felt something. We have to wait until tomorrow. In this situation, as the coach, I have to manage it. I'm thinking about all the injured players.
"I'm worried about them; I was injured myself and I know what it's like. But we have to focus on the next match now. I wouldn't say I'm worried, but I have a lot on my mind."