Fernandinho started the 2012–13 season by assisting Douglas Costa for the second goal in a 2–0 Super Cup victory over Metalurh Donetsk. This marked his third success in the Super Cup with Shakhtar. He assisted Yevhen Seleznyov's goal in the 3–1 victory over Hoverla Uzhhorod. He netted a late goal to earn Shakhtar three points in a 1–0 win over Kryvbas. He assisted Henrikh Mkhitaryan for the first goal in a 4–1 victory over Vorskla Poltava. On 23 September, he scored a goal in a 4–1 Ukrainian Cup last 32 victory against Dynamo Kyiv and was named man of the match. He assisted Henrikh Mkhitaryan for the second goal in a 2–0 victory against Metalist Kharkiv on 7 October. Fernandinho scored the second goal in a 2–1 victory against English side Chelsea in the Champions League group stage on 23 October, shooting low with his right foot into the bottom corner.