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| 01.04.1999 | 19:00 | Arminia Bielefeld | - | Rot-Weiß Oberhausen | 2:0 (1:0) | |
| 19:00 | SpVgg Unterhaching | - | FC St. Pauli | 2:1 (1:0) | ||
| 19:00 | TeBe Berlin | - | Stuttgarter Kickers | 0:2 (0:1) | ||
| 04.04.1999 | 15:00 | SSV Ulm 1846 | - | FC Gütersloh | 1:1 (1:0) | |
| 15:00 | Hannover | - | Mainz | 3:2 (2:1) | ||
| 15:00 | SpVgg Greuther Fürth | - | KFC Uerdingen 05 | 0:0 (0:0) | ||
| 15:00 | Colonia | - | Energie Cottbus | 2:2 (1:1) | ||
| 15:00 | SG Wattenscheid 09 | - | Fortuna Düsseldorf | 2:0 (1:0) | ||
| 05.04.1999 | 20:15 | Karlsruher SC | - | Fortuna Köln | 4:2 (1:0) |
| » 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 | 24 | 15 | 3 | 6 | 32:16 | 16 | 48 |
| 2 |
|
SpVgg Greuther Fürth | 24 | 13 | 7 | 4 | 33:15 | 18 | 46 |
| 3 |
|
Arminia Bielefeld | 24 | 14 | 4 | 6 | 40:23 | 17 | 46 |
| 4 |
|
TeBe Berlin | 24 | 12 | 5 | 7 | 39:32 | 7 | 41 |
| 5 |
|
Karlsruher SC | 24 | 13 | 1 | 10 | 42:33 | 9 | 40 |
| 6 |
|
SSV Ulm 1846 | 24 | 10 | 10 | 4 | 45:38 | 7 | 40 |
| 7 |
|
Hannover | 24 | 11 | 4 | 9 | 35:27 | 8 | 37 |
| 8 |
|
Mainz | 24 | 10 | 5 | 9 | 34:34 | 0 | 35 |
| 9 |
|
Stuttgarter Kickers | 24 | 9 | 5 | 10 | 23:30 | -7 | 32 |
| 10 |
|
Fortuna Köln | 24 | 8 | 7 | 9 | 37:41 | -4 | 31 |
| 11 |
|
Colonia | 24 | 7 | 9 | 8 | 29:37 | -8 | 30 |
| 12 |
|
Rot-Weiß Oberhausen | 24 | 6 | 10 | 8 | 29:35 | -6 | 28 |
| 13 |
|
FC St. Pauli | 24 | 7 | 6 | 11 | 28:34 | -6 | 27 |
| 14 |
|
Energie Cottbus | 24 | 4 | 10 | 10 | 25:31 | -6 | 22 |
| 15 |
|
SG Wattenscheid 09 | 24 | 5 | 7 | 12 | 20:32 | -12 | 22 |
| 16 |
|
FC Gütersloh | 24 | 5 | 7 | 12 | 30:43 | -13 | 22 |
| 17 |
|
Fortuna Düsseldorf | 24 | 3 | 12 | 9 | 27:37 | -10 | 21 |
| 18 |
|
KFC Uerdingen 05 | 24 | 4 | 8 | 12 | 26:36 | -10 | 20 |
