| Rank | Team | Pts. | Yellow cards | Second yellow cards | Straight red cards |
|---|---|---|---|---|---|
| 1 | SpVgg Unterhaching | 37 | 37 | 0 | 0 |
| 2 | FV Illertissen | 68 | 65 | 1 | 0 |
| 3 | FC Augsburg | 73 | 55 | 1 | 3 |
| 4 | TSV 1860 Munich | 74 | 58 | 2 | 2 |
| 5 | Wacker Burghausen | 75 | 62 | 1 | 2 |
| 5 | SV Schalding-Heining | 75 | 65 | 0 | 2 |
| 7 | Bayern Munich | 76 | 68 | 1 | 1 |
| 8 | TSV 1860 Rosenheim | 77 | 71 | 2 | 0 |
| 9 | VfR Garching | 79 | 76 | 1 | 0 |
| 10 | SpVgg Greuther Furth | 86 | 64 | 4 | 2 |
| 11 | SpVgg Bayern Hof | 87 | 66 | 2 | 3 |
| 12 | FC Ingolstadt | 90 | 74 | 2 | 2 |
| 13 | 1. FC Nuremberg | 93 | 67 | 2 | 4 |
| 14 | FC Memmingen | 99 | 80 | 3 | 2 |
| 15 | SpVgg Upper Franconia Bayreuth | 100 | 82 | 1 | 3 |
| 16 | 1. FC Schweinfurt 05 | 109 | 80 | 3 | 4 |
| 17 | SV Seligenporten | 116 | 97 | 3 | 2 |
| 17 | TSV Buchbach | 116 | 89 | 4 | 3 |