At the end of the 2011–12 season, SV Sandhausen and VfR Aalen were directly promoted to the 2012–13 2nd Bundesliga.
The two promoted teams were replaced by Alemannia Aachen and Hansa Rostock, who finished in the bottom two places of the 2011–12 2nd Bundesliga table and thus were directly relegated.
On the other end of the table, Rot-Weiß Oberhausen, FC Carl Zeiss Jena and SV Werder Bremen II were relegated to the 2012–13 Fußball-Regionalliga; Oberhausen entered the newly formed Regionalliga West, with Jena going to the Regionalliga Nordost and Werder Bremen reserves being admitted to the Regionalliga Nord.
A further place in the league was available via a two-legged play-off between third-placed 2011–12 3rd Liga team Jahn Regensburg and 16th-placed 2011–12 2.
Being a charter member of the 3rd Liga, Regensburg returned to the second level after eight years in the third tier of the German football league system; in turn, Karlsruhe gave their debut in the 3rd Liga after finishing a three-year 2nd Bundesliga spell, returning to the third level for the first time since the 2000–01 season in the process.