The Germans, who face Hungary on Friday in Leipzig before travelling to England next week, will be without the pair who were ruled out with COVID-19 infections on Wednesday.
"It was good preparation. We don't know what will happen in Qatar and something like that could happen to us there as well," Flick told a news conference. "We have to always be able to react, to deal with the situation in the best possible way."
Hours after the cases were known, Flick nominated Maximilian Arnold and keeper Oliver Baumann as replacements.
"We are happy that both were fully in training (despite the international break)."
Flick will start with Marc-Andre ter Stegen in goal against Hungary as he looks to fine tune his team ahead of the World Cup, which starts in less than two months.
Four-time world champions Germany are desperate to make amends following their shock first round exit at the 2018 World Cup.
"It is good to have these matches now. We will use these games to fine tune our game. We have said that it would be a statement if we could top our Nations League group.
"So we want to get to the (Nations League) final four. It is up to us and we are well prepared."
