Following his injury in the Euro 2012 tournament, it was revealed that Papadopoulos had torn his ACL. After an eight-month absence, Papadopoulos returned to play by entering as a substitute for Kostas Manolas on the 46th minute of a 1–0 victory over Kavala F.C. on 30 January 2013. On 10 March 2013 he managed to score 2 goals against AEK Athens F.C. in a 3–0 home win. With that win Olympiacos claimed the 40th champion in his history. He also scored in the final match of the season, against Panionios GSS in a 2–1 home win after an assist of Ariel Ibagaza.