A double from Jules Kounde saw Barca win 2-1 on the night, with Yamal visibly angry when taken off by Flick for Roony Bardghji in the final minutes of normal time.
Flick said afterwards: "He had a slight disappointment, but he had a yellow card and we needed fresh legs. It's not a problem.
"It is what it is. I understand him; everyone wants to play, and he believes he can play 100 minutes. He's young. It's a good attitude. I have no problem with it. I was a player myself. I accept it."
He added, "I'm happy, these are three important points. We're back. The match wasn't easy. We created quite a few chances and opportunities."
On two-goal Kounde, Flick said: "I didn't expect it. Their mentality is important for us. But I'm very happy. We have the space we needed. They know what needs to be done.
"I also congratulate my staff, who have done a good job. I'm happy to have come back."