Pedri laid on Lamine Yamal's second-half winner on the night.
Flick said afterwards, "It's not easy to play here. I think we had to manage our minutes after Tuesday's game. I really value the win. And we kept a clean sheet.
"I said it before, Pedri makes everyone better. He changes the game. He connects very well. (Dani) Olmo also played better in the second half. But the important thing is that everyone fought as a unit."
On the clean sheet, Flick continued: "I think when we play our style, we sometimes get through. It depends on the whole team; we all defend. A clean sheet gives confidence and helps our philosophy."
On matchwinner Lamine Yamal, he added: "He didn't have his best game, but his goal decided it. When he has space, opportunities... he trains a lot. It's good that he can solve the game in a situation."