On 24 May 2013, the eve of the 2013 Champions League Final between Bayern Munich and Borussia Dortmund, Papastathopoulos completed a €9.5 million transfer to Dortmund, agreeing to a five-year contract through to 2018. Upon signing, he spoke about the deal, saying, "Money did not play a role in my decision to join Dortmund. My own future was all that mattered and I am convinced that I made the right decision." With centre-back Felipe Santana departing Dortmund for Schalke 04, Papastathopoulos began as the effective third-choice behind tandem Neven Subotić and Mats Hummels. Borussia Dortmund Sporting Director Michael Zorc expressed his satisfaction with the deal: "We are delighted that Sokratis has decided to join Borussia Dortmund. He is a flexible player capable to play in a variety of positions in defence who we believe has tremendous potential."