SC Freiburg were the first team to win promotion to Bundesliga 2009–10 after securing the 2.
FSV Mainz 05 were also directly promoted as runners-up after a 4–0 home victory over Rot-Weiß Oberhausen.
FC Nürnberg, Hansa Rostock and MSV Duisburg, which were relegated at the end of the 2007–08 Bundesliga season.
Kickers Offenbach, Erzgebirge Aue, FC Carl Zeiss Jena and SC Paderborn 07 were relegated to the newly formed 3.
Rot Weiss Ahlen and Rot-Weiss Oberhausen earned promotion in the Regionalliga Nord while FSV Frankfurt and FC Ingolstadt 04 were promoted from the Regionalliga Süd.
Paderborn won both matches on an aggregated score of 2–0 and thus secured promotion to 2.