Barcelona maintained their perfect start in LaLiga with a sixth consecutive victory but the win was marred by possibly a season-ending injury of their German keeper.
"It looks like a serious injury, he felt it, you could see it on the pitch," Flick told a press conference.
Ter Stegen fell badly after jumping for a ball just before halftime and was visibly in pain as he was carried off the pitch on a stretcher.
All of the goalkeeper's weight fell on his right leg as he injured the same knee on which he already underwent two surgeries over the recent years, and another surgery could prove season-ending, Spanish media reported.
Asked whether he had already thought of a replacement, Flick said: "I don't like this question right after the game. First we have to see what happens with Marc, he's our captain.
"I'm very sad about what happened. Please understand that I don't want to answer this question. I haven't been able to speak to Ter Stegen."
The German keeper had his hands full in a highly entertaining clash that saw a total of 30 goal attempts, 14 of them on target.
"This victory is for Ter Stegen. He's currently in the hospital," said striker Robert Lewandowski, who found the net twice inside 35 minutes to give Barcelona the lead.