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| 30.04.1999 | 19:00 | SSV Ulm 1846 | - | Rot-Weiß Oberhausen | 1:0 (1:0) | |
| 19:00 | FC St. Pauli | - | FC Gütersloh | 1:0 (1:0) | ||
| 19:00 | Colonia | - | KFC Uerdingen 05 | 4:0 (0:0) | ||
| 02.05.1999 | 15:00 | Arminia Bielefeld | - | Stuttgarter Kickers | 1:2 (1:0) | |
| 15:00 | SpVgg Unterhaching | - | Fortuna Düsseldorf | 1:0 (0:0) | ||
| 15:00 | Hannover | - | Fortuna Köln | 3:3 (2:1) | ||
| 15:00 | Mainz | - | Energie Cottbus | 0:0 (0:0) | ||
| 15:00 | SG Wattenscheid 09 | - | SpVgg Greuther Fürth | 1:1 (0:0) | ||
| 03.05.1999 | 20:15 | Karlsruher SC | - | TeBe Berlin | 0:0 (0:0) |
| » 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 | 28 | 17 | 4 | 7 | 37:20 | 17 | 55 |
| 2 |
|
Arminia Bielefeld | 28 | 16 | 5 | 7 | 48:26 | 22 | 53 |
| 3 |
|
SpVgg Greuther Fürth | 28 | 13 | 9 | 6 | 37:21 | 16 | 48 |
| 4 |
|
TeBe Berlin | 28 | 14 | 6 | 8 | 42:34 | 8 | 48 |
| 5 |
|
SSV Ulm 1846 | 28 | 12 | 11 | 5 | 51:43 | 8 | 47 |
| 6 |
|
Hannover | 28 | 13 | 6 | 9 | 43:31 | 12 | 45 |
| 7 |
|
Karlsruher SC | 28 | 14 | 3 | 11 | 45:36 | 9 | 45 |
| 8 |
|
Mainz | 28 | 11 | 7 | 10 | 37:37 | 0 | 40 |
| 9 |
|
Stuttgarter Kickers | 28 | 10 | 7 | 11 | 29:37 | -8 | 37 |
| 10 |
|
Fortuna Köln | 28 | 9 | 9 | 10 | 44:47 | -3 | 36 |
| 11 |
|
Colonia | 28 | 9 | 9 | 10 | 38:42 | -4 | 36 |
| 12 |
|
FC St. Pauli | 28 | 9 | 6 | 13 | 32:41 | -9 | 33 |
| 13 |
|
Rot-Weiß Oberhausen | 28 | 6 | 12 | 10 | 30:41 | -11 | 30 |
| 14 |
|
Energie Cottbus | 28 | 6 | 11 | 11 | 32:35 | -3 | 29 |
| 15 |
|
FC Gütersloh | 28 | 7 | 7 | 14 | 32:45 | -13 | 28 |
| 16 |
|
SG Wattenscheid 09 | 28 | 6 | 9 | 13 | 23:34 | -11 | 27 |
| 17 |
|
Fortuna Düsseldorf | 28 | 4 | 12 | 12 | 29:42 | -13 | 24 |
| 18 |
|
KFC Uerdingen 05 | 28 | 5 | 9 | 14 | 27:44 | -17 | 24 |
