The 18-year-old was ruled out for the rest of the season with a hamstring injury, which he suffered on Wednesday as Barcelona beat Celta Vigo in LaLiga.
Lamine Yamal won and converted a penalty to help his side stay nine points clear of Real Madrid at the top of the table, but immediately went down injured and was substituted.
"It's not easy this situation for us, but also for him," Flick told reporters.
"He knows it was his first muscle injury. What I can feel is that he is very focused. He has the motivation - he is out for us, but I think for the World Cup he will be there and he will be stronger, (he will) come back stronger than now."
Lamine, who finished second in the Ballon d'Or vote last year and helped Spain triumph at EURO 2024, has been a key figure in Barcelona's attempt to defend their LaLiga title.
Flick said that Lamine may have been hurt by the foul which brought him down for the penalty, but that he did not realise the situation he was in, as he had not suffered such an injury before.
"He felt something after the foul, but I think it was not so much. And he decided to kick the penalty, and after that it's maybe more," said Flick.
"He never had a muscle injury before, so it's also part of learning about the signal the body gives you.
"It's not so easy because he is really young, but in the end it's an experience. And this is what he has to learn."
Lamine has scored 24 goals and provided 18 assists this season for Barca across all competitions and has nine goals in his last 12 league matches.
"I really appreciate a lot the last few weeks. He was on an unbelievable level. He's more mature than 18," added Flick.
"He's clever, he's smart, and he knows what he wants. Of course, now this injury affects him also... but then you have to focus on what's going on in the process to come back, to get fitter and fitter and better and better."
Barcelona visit Getafe on Saturday, while Madrid travel to Real Betis on Friday.