The second placed teams of each Landesliga division, together with the 15th placed team from the Bayernliga Nord and the 15th and 16th placed team Bayernliga Süd entered a play-off for two more places in the 2013–14 Bayernliga. All three Bayernliga clubs were relegated while the Landesliga teams of SV Raisting and VfR Garching were promoted:
