Barca won 4-2, with Fermin Lopez (2), Dani Olmo and Robert Lewandowski on the scoresheet.
Afterwards, Flick said: "After conceding two goals from set pieces, we came back, and that's good. It wasn't easy to play today. It was very cold, and Slavia played very well.
"They're a physical team, with dangerous transitions and balls. We were better in the second half."
Asked about Fermin's performance, the German continued: "He's very good. But Dani Olmo also did well when he came on, scoring an important goal. Lewandowski also fought hard. It was news that Fermín didn't go to Chelsea.
"It's important for Barcelona that he stayed, and for him too. I value what he's done."
One headache for Flick was Pedri being forced off on the hour mark. The Barca coach confirmed it was a hamstring issue for the midfielder.
He added, "I don't know how he is; he has a hamstring problem and needs to undergo tests. These things happen. I don't know exactly how many weeks he'll be out. It's not good news.
"But Dani came on for him and scored. And (Marcus) Rashford also played well."