The 24-year-old striker chose to seek regular game time elsewhere after the Blues brought in Olivier Giroud from London rivals Arsenal on transfer deadline day.
Batshuayi made just 10 starts in all competitions for Antonio Conte's side this term, but still managed to bag 10 goals from his 25 appearances in total and netted a brace in the 3-0 win over Newcastle on Sunday.
BVB were in the market for a new frontman after selling Pierre-Emerick Aubameyang to the Gunners earlier on Wednesday, which opened the door for Giroud to move to Stamford Bridge.
Dortmund sporting director Michael Zorc told the club's official website: "Michy is a young, very interesting striker who boasts a good goalscoring record and has shown his extraordinary quality at Chelsea and Olympique Marseille, in the Belgian league and while playing for the national team."
Batshuayi added: "In order to achieve my big objective, I want to play as much as possible and score many goals. The World Cup is taking place in the summer."