Barca took control of their round 16 tie after Raphinha struck on the hour mark for the 1-0 win in Portugal. Making the victory all the more impressive was Barca played with ten men after Pau Cubarsi's 22nd minute dismissal.
A beaming Flick said afterwards: "I'm very proud, after playing from the 22nd minute with one less player, it's a great performance. They ran a lot.
"I'm satisfied with the victory. I'm very proud of the team because we defended very well and managed the match well. It's a very big victory.
"In a 95- or 100-minute game, it's difficult for the fans but also for the coaches. I'm proud, they did fantastic. I said hats off to them. After being reduced to 10 men in the 22nd minute, it wasn't easy.
"It's a great victory for us, but we know that there's still the return leg, that Benfica is a great team and that we have to be careful."
On goalkeeper Wojciech Szczesny after his clean sheet, Flick also said: "I'm very happy. It's important when you keep a clean sheet playing with 10 men. He had a fantastic performance. He saved us.
"I'm happy for him and for the team. Every game he's getting more confident and we're defending better. He's a fantastic goalkeeper. I've already said that he had a fantastic game, but not just him. Everyone fought hard."