Dortmund's Lucas Barrios of Paraguay with Egyptian Mohamed Zidan
Paraguay international Barrios, who had only recently returned from an injury that saw him miss the start of the season, broke off training on Monday and tests showed a minor muscle injury.
“Lucas Barrios will remain in Dortmund along with Patrick Owomoyela,” Dortmund said before departing for Athens.
Owomoyela, who is also just back from a long injury break, suffered a partial muscle tear in their 2-0 win over Werder Bremen on Friday.
Dortmund are third in Group F with one point from two games, ahead of Olympiakos, who lost both their opening games. Olympique Marseille lead the standings with six points, two ahead of Arsenal.