Leitner made his first start of the 2012–13 season in a 2–1 loss against Bayern Munich in the DFL-Supercup. After the departure of Shinji Kagawa, he received more game time, making 30 appearances. Due to the impressive performances of Mario Götze, however, only ten of these were as a starter and he spent most of the 2012–13 season on the substitutes bench. He appeared as an unused substitute in the UEFA Champions League Final against Bayern Munich. He made three assists with no goals scored. Leitner hinted at leaving Borussia Dortmund to get first team football in the 2013–14 season.