The Bundesliga giants have confirmed the signing of the Armenia international on a four-year deal
The German side already confirmed on Monday that they had agreed terms with Shakhtar and the 24-year-old has now signed a contract until the summer of 2017 with his new club.
Dortmund were in the market for a new attacking midfielder due to the departure of Mario Gotze to Bayern Munich earlier this summer and they see Mkhitaryan as the perfect replacement.
"We are very pleased to have strengthened our attacking midfield with a superb signing like Henrik Mkhitaryan," sporting director Michael Zorc told the club's official website.
BVB CEO Hans-Joachim Watzke was equally satisfied with the arrival of Mkhitaryan, but admitted that signing the Armenia star was not an easy task.
"This was not an easy transfer, but we were determined to get our man - and now we have him," stated Watzke.
The attacking midfielder is BVB's third signing of the summer transfer window after the previous capture of Sokratis Papastathopoulos from Werder Bremen and Pierre-Emerick Aubameyang from Saint-Etienne.
Mkhitaryan will be wearing the No.10 jersey at Borussia.