The midfielder won't be seen again until early 2026 after going under the knife this week.
Ahead of their clash with Real Oviedo, Flick commented on the decision for Gavi to undergo his operation.
He said, "When you receive this information, you say, bad news, but in the end it is the best for him. We have to take care of him, he has to go step by step and it was the way for him to have a long career.
"He must be 100% fine and then step by step. He is a player with a big heart, I am very happy to have him on the team. It is not easy for the team, but we will be supporting him to return to his best level. I think it is not easy for a young player to receive this news.
"He was fine, but we have to help him. He is very professional, especially with his attitude, he is top level. It's not easy, but if anyone can overcome it, it's him."