The 24-year-old has fallen out of favour with coach Thomas Tuchel after a string of below-par performances and is struggling with a leg injury, which kept him out of Saturday's shock 2-1 defeat at Bundesliga bottom side Darmstadt.
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"For him, the game in Lisbon came a bit too soon," Dortmund's director of sport Michael Zorc told BVB.de.
Injury and loss of form mean Goetze, who scored the winning goal in the 2014 World Cup final, has played just 24 minutes of football so far in 2017.
Dortmund have been boosted with the return of both captain Marcel Schmelzer and Lukasz Piszczek, who missed the Darmstadt defeat with injury.
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Wingers Ousmane Dembele and Marco Reus have both shaken off knocks picked up in Darmstadt.
Tuesday's fixture at the Estadio da Luz will be the first meeting between Benfica and Dortmund since the first round of the 1963/64 European Cup, a tie the German club won 6-2 on aggregate.
The second leg in Germany is scheduled for March 8.
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