Reus, who signed a new long-term contract with Dortmund last month, had to be helped from the field in the first half of the last 16 tie due to an apparent injury to his left knee.
The 25-year-old has been plagued by injuries in recent times and was forced to miss Germany's 2014 World Cup success after tearing ligaments in his left ankle.
He subsequently suffered similar problems in September and November last year, leading to further layoffs.
Following Reus' latest setback, the German Football Association (DFB) tweeted a 'get well soon' message to the forward.
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