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Schlotterbeck started Germany's 2-0 win over Peru last week, but he has been ruled out of Wednesday's (AEDT) friendly with Belgium in Cologne due to a thigh injury.
However, the 23-year-old – who has both played in (36) and started (33) the most games of any BVB player this season – is expected to be available for Saturday's trip to Bayern.
"We didn't want to take any risks with him," Flick said. "It's nothing serious and in two or three days he'll be back on the pitch."
Bundesliga leader Dortmund heads into Der Klassiker a point better off than Bayern, who sacked Julian Nagelsmann and replaced him with Thomas Tuchel last week.
Chelsea attacker Kai Havertz was another withdrawal from the Germany squad due to illness ahead of the prestige friendly with Belgium at RheinEnergieStadion.
Flick announced Thilo Kehrer and Serge Gnabry will come into the starting line-up in place of Schlotterbeck and Havertz respectively, with "one or two" other changes possible.
Belgium kicked off a new era under Domenico Tedesco with a 3-0 Euro 2024 qualifying win over Sweden thanks to Romelu Lukaku's hat-trick in Stockholm.
The Red Devils are in somewhat of a transition period, with a number of their 'Golden Generation' making way after their recent World Cup group-stage exit.
Germany head coach Flick expects the nation ranked fourth in the world to pose more of a challenge than Peru.
"We started the new year with a win, but in Belgium we have an opponent of a different calibre," he said.
"They have a new coach and a new spirit. You can see immediately they have outstanding footballers in their ranks.
"They are able to defend compactly, but they are also convincing in an attacking sense when they have possession of the ball. They scored brilliant goals against Sweden.
"Even under pressure they always find good solutions. In terms of football, they are one of the best teams and will be a good opponent for us to measure ourselves against."