The Brazilian has sealed a three-year contract at the Veltins Arena, with Jens Keller's side set to pay just one million euros for his services
The Brazilian defender has found it hard to break into the BVB first team during his five years at Signal Iduna Park, having found himself firmly behind Mats Hummels and Neven Subotic in the pecking order.
With Christoph Metzelder - another former Dortmund defender - having announced his retirement earlier this week, Jens Keller's side has been in the market for a new center back.
Meanwhile, another Schalke defender, Kyriakos Papadopoulos has also been heavily linked with a move away from the club, leaving Jens Keller's side short of options at the back.
Santana has long been linked with a move to the Veltins Arena and has now sealed a contract until 2016 worth around three million euros per season for a fee of one million euros, which is his release clause.
With Hummels having sustained an ankle injury during the 2-1 loss to Hoffenheim on Saturday, Santana has a chance of representing Dortmund in the Champions League final against Bayern Munich on May 25.
His stoppage-time goal against Malaga in the second leg of the Champions League quarterfinal this season dramatically ensured Dortmund secured a spot in the last four of the competition.