The on-loan Chelsea striker left the Veltins-Arena on crutches and is due to undergo a scan on Sunday evening to reveal the full extent of the damage.
Belgium international Batshuayi, who has hit seven goals for Dortmund since arriving in January, is now considered a major doubt for the World Cup finals over fears that he may have broken his ankle in the challenge from Benjamin Stambouli.
"He is in great pain," Stoger told reporters after the match. "It looked like he could be out for a long time. I hope it's not that bad."
Dortmund lost the Revierderby 2-0 to slip four points behind their rivals in the race for a runners-up spot.