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| 07.05.1999 | 19:00 | Stuttgarter Kickers | - | Colonia | 2:0 (1:0) | |
| 19:00 | Fortuna Köln | - | SSV Ulm 1846 | 2:2 (0:1) | ||
| 19:00 | Fortuna Düsseldorf | - | Hannover | 1:1 (0:0) | ||
| 09.05.1999 | 15:00 | SpVgg Greuther Fürth | - | Karlsruher SC | 1:2 (0:1) | |
| 15:00 | Energie Cottbus | - | FC St. Pauli | 0:3 (0:3) | ||
| 15:00 | Rot-Weiß Oberhausen | - | Mainz | 2:1 (1:1) | ||
| 15:00 | FC Gütersloh | - | SG Wattenscheid 09 | 2:1 (1:1) | ||
| 15:00 | KFC Uerdingen 05 | - | SpVgg Unterhaching | 3:0 (1:0) | ||
| 10.05.1999 | 20:15 | TeBe Berlin | - | Arminia Bielefeld | 1:1 (1:1) |
| » Clasificación | En casa | Fuera de casa | 1.ª vuelta | 2.ª vuelta | 1.ª parte | 2.ª parte |
| # | Equipo | P | V | E | D | Goles | DG | Pun. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
SpVgg Unterhaching | 29 | 17 | 4 | 8 | 37:23 | 14 | 55 |
| 2 |
|
Arminia Bielefeld | 29 | 16 | 6 | 7 | 49:27 | 22 | 54 |
| 3 |
|
TeBe Berlin | 29 | 14 | 7 | 8 | 43:35 | 8 | 49 |
| 4 |
|
SpVgg Greuther Fürth | 29 | 13 | 9 | 7 | 38:23 | 15 | 48 |
| 5 |
|
Karlsruher SC | 29 | 15 | 3 | 11 | 47:37 | 10 | 48 |
| 6 |
|
SSV Ulm 1846 | 29 | 12 | 12 | 5 | 53:45 | 8 | 48 |
| 7 |
|
Hannover | 29 | 13 | 7 | 9 | 44:32 | 12 | 46 |
| 8 |
|
Mainz | 29 | 11 | 7 | 11 | 38:39 | -1 | 40 |
| 9 |
|
Stuttgarter Kickers | 29 | 11 | 7 | 11 | 31:37 | -6 | 40 |
| 10 |
|
Fortuna Köln | 29 | 9 | 10 | 10 | 46:49 | -3 | 37 |
| 11 |
|
Colonia | 29 | 9 | 9 | 11 | 38:44 | -6 | 36 |
| 12 |
|
FC St. Pauli | 29 | 10 | 6 | 13 | 35:41 | -6 | 36 |
| 13 |
|
Rot-Weiß Oberhausen | 29 | 7 | 12 | 10 | 32:42 | -10 | 33 |
| 14 |
|
FC Gütersloh | 29 | 8 | 7 | 14 | 34:46 | -12 | 31 |
| 15 |
|
Energie Cottbus | 29 | 6 | 11 | 12 | 32:38 | -6 | 29 |
| 16 |
|
SG Wattenscheid 09 | 29 | 6 | 9 | 14 | 24:36 | -12 | 27 |
| 17 |
|
KFC Uerdingen 05 | 29 | 6 | 9 | 14 | 30:44 | -14 | 27 |
| 18 |
|
Fortuna Düsseldorf | 29 | 4 | 13 | 12 | 30:43 | -13 | 25 |
