Dani Olmo and Ferran Torres struck for Barca on the evening.
Flick said: "We didn't play a very good game. But we won 0-2 and that's good. With the three points, the road back is easier to face. At half-time, we explained to them what to do better in some situations and we talked about what wasn't being done as we wanted.
"The players were good. We're very happy with the three points, but not so much with our performance. It's normal that I'm tired. But we're still leaders in LaLiga. And in the end we want to progress and be better.
"We lacked control and possession. We didn't play as we would have liked. We lost balls and were inaccurate. In the first half, we had more problems than usual."
On Olmo, he added: "The goal is very important, for us and for him. He didn't play more before because he was injured and the others were also a little better in terms of fitness. We are happy for him.
"It was a good goal for him. And also for Ferran, who also came off the bench. Everyone was also involved in defence, and we kept a clean sheet again, and that is good."