The Belgium international, who has impressed since joining BVB on loan from Chelsea during the January transfer window, sustained the problem during Sunday's 2-0 defeat to Schalke in the Ruhr derby.
The 24-year-old landed awkwardly following a challenge with Schalke's Benjamin Stambouli late in the contest and left the field on a stretcher.
Dortmund have now confirmed the frontman is likely to miss the rest of the domestic season, which means he may well have played his last game for the club although they do expect him to be fit for Belgium's World Cup campaign.
"Michy Batshuayi contracted an ankle injury during the derby game at Schalke and is likely to miss the remainder of the season," Dortmund announced on Twitter.
"An appearance for the Belgian national team at the World Cup in Russia remains a possibility. Get well soon, Michy!"
Batshuayi has scored nine goals in 14 appearances since joining Dortmund and his absence will be a blow to Peter Stoger's side, who are still not assured of a top-four finish in the Bundesliga.