Batshuayi was was taken off on a stretcher late on in the defeat to Schalke, having appeared to roll his ankle.
The 24-year-old posted on his social media channels: "Well its not good news for now, my season is probably over, and I wont be able to pay @bvb09 back for their confidence."
Borussia Dortmund also confirmed the news and tweeted: "@mbatshuayi has suffered an ankle injury in the derby at @s04 and is likely to be out for the rest of the season. Playing for the Belgian national team at the World Cup in Russia is possible. Get well soon, Michy!"
With the World Cup in two months' time, Batshauyi could now miss out on joining up with Roberto Martinez's side.
On social media, Batshuayi added: "Thank you all the amazing amount of love I received since yesterday. Wishing my teammates the best for the final days. See you soon."