The 22-year-old has scored 17 goals in 92 J.League matches. He joined Oita Trinita in 2008, moving to Cerezo Osaka in 2010.
His transfer fee to the Bundesliga side is estimated at about €1 million and he has signed a three-year contract.
Kiyotake has played in five games without scoring a goal for Japan's senior side. He is also a member of the Olympic squad seeking the country's first football medal since they won bronze at the 1968 Mexico City Games.
Japanese players in Germany's professional leagues include Borussia Dortmund star Shinji Kagawa, who appears set to move to England, Stuttgart striker Shinji Okazaki and Wolfsburg midfielder Makoto Hasebe.