Yamal, who grabbed the spotlight as he helped Spain win their fourth European Championship title in July, scored twice in the first half before Dani Olmo and Pedri secured the win with Flick's side maintaining their unbeaten start to the league season.
"I'm very happy about Lamine's two goals, he's very young but he's really incredible, a difference maker in such a young age," Flick told Movistar Plus.
"Having him is key for us not only because of his quality but he also presses very well high. He combines talent and pressure and that's massive for us. He is outstanding.
"It was a tough game, Girona played well but we started very well too and we deserved to win."
Hansi Flick's Barcelona top the LaLiga standings with 15 points, four ahead Real Madrid and Villarreal. Last year's surprise package Girona are seventh with seven points.
Barca avenged their two losses to Girona last season, both by a 4-2 result. It was a dominant performance by the Catalonia giants whose relentless high press was too much for the locals to handle.
Now Barca will hope to carry their domestic momentum into the Champions League, where they will face Monaco away on Thursday.
"We have trained very hard for this and we need to keep going. This last week we have prepared well, but we do it for every game we play because we always want to win, we are in a good moment and we can't stop," Flick said.
"It won't be easy against Monaco but we're taking it one game at a time and we're really excited, we're all looking forward to it."
