They were replaced by FC Ingolstadt 04 and SV Wehen Wiesbaden, who finished in the bottom two places after the previous season.
VfR Aalen and Stuttgarter Kickers were relegated after finishing the 2008–09 season in the bottom two places.
18th-placed SV Wacker Burghausen were eventually spared from relegation after 5th-placed Kickers Emden voluntarily retracted their application for a license because of financial issues.
The three relegated teams were replaced by the champions of the three Regionalliga divisions, Holstein Kiel (North), Borussia Dortmund II (West) and 1.
Source: Kicker magazine (in German) Björn Lindemann was named as player of the season