Both Akanji and Batshuayi could make their Bundesliga debuts on Friday at bottom side Cologne.
Dortmund head coach Peter Stoeger could only register one of his new recruits for the Europa League after signing Akanji from Basel and Batshuayi from Chelsea.
The new recruits had already played in the Champions League this season for their respective clubs, meaning Dortmund could not register both for the Europa League.
Belgium striker Batshuayi was signed on loan until the end of the season after Arsenal paid a club record £56 million ($79m, 63m euros) for Dortmund’s top-scorer Pierre-Emerick Aubameyang.
Discarding Akanji for their European campaign could be a gamble after already losing two centre-backs in the January transfer window.
Ex-Barcelona defender Marc Bartra joined Real Betis and Neven Subotic moved to French league side St Etienne.
After finishing third in their Champions League group behind Tottenham Hotspur and Real Madrid, Dortmund face Atalanta in the last 32 of the Europa League.
They host the Italians on February 15 with the return leg on February 22.
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