Amid reports of him wanting to leave Dortmund in January, Adeyemi was hooked in the 60th minute of Friday's game.
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The young forward was furious and made a move to go straight to the dressing room before being blocked from doing so by sporting director Sebastian Kehl.
Kehl later explained: "It (the substitution) was totally justified. Karim didn't play a good game.
"The coach doesn't want to see it, no one wants to see it. It's inappropriate and Karim knows it. For his actions, he will be fined."
Coach Niko Kovac also said: "He wasn't good today, so the substitution is justified. You also have to be aware of your own mistakes."
Adeyemi, 23, is being linked with the likes of Liverpool, Manchester United and Juventus this season.