The win extended Barcelona's lead at the top of La Liga after second-half strikes from Raphinha and Fermin Lopez overturned the hosts' advantage, with Ter Stegen in fine form after a seven-month absence.
"We'll see about Marc, he did well today, but Szczesny will play in the Champions League and against Real Madrid," Flick told reporters.
The German tactician made nine changes to his starting line-up for the Valladolid game, with Tuesday's Champions League clash and next weekend's showdown with Madrid looming large in terms of player fatigue.
"I'm not disappointed. When you make that many changes, it's not easy for the players, they're young. I believe in them. I have confidence. When there is a lot of rotation, the level is different.
"I was able to rest some players and give some minutes to others. It wasn't easy. There were a few mistakes, quick transitions, but (Ronald) Araujo and (Andreas) Christensen had a good game and Ter Stegen too," the manager added.
Despite trailing at half-time, Flick was pleased with the performance of his side. He praised Raphinha's and hinted that Fermin Lopez could start for Milan: "He is a player who always has a chance to start. He can play in different positions.
"The goal is three points and I'm satisfied that we got them. Mission accomplished," Flick added.