The 26-year-old has signed a four-year contract with BVB after a deal in the region of €20 million (£17.6m) was reportedly agreed between the clubs.
The Denmark international, who had been linked with a transfer to the Premier League, moves to Signal Iduna Park only 18 months on from joining Werder from Copenhagen.
"Borussia Dortmund have always had a top-class experience with Denmark internationals," sporting director Michael Zorc told the club's official website.
"Thomas Delaney is a physically and mentally strong player. He will enrich our game with his physical presence."
Delaney suggested he turned down approaches from England's top flight in order to join Dortmund.
"It was always a big desire of mine to play in the Premier League, and I had offers," he said. "But when Borussia Dortmund were mentioned, I didn't have to think long.
BVB verpflichtet Thomas #Delaney!— Borussia Dortmund (@BVB) June 7, 2018
Der dänische Nationalspieler @delaneydk kommt von @werderbremen und hat bei Borussia Dortmund einen Vertrag bis 2022 unterschrieben! #Delaney2022 - alle Infos https://t.co/3pWkMVcsr6 pic.twitter.com/Z2LOCvWgtl
"For me, BVB are one of the top 10 clubs in Europe and one of the top two in Germany - and the stadium is the best in Europe."
Delaney made 32 appearances in the Bundesliga last season, scoring three goals.