| Place | Performance | Athlete | Team |
| 1 | 0:46.55 | VAN DER WALT - TJ | MADIBAZ |
| 2 | 0:46.70 | MESHACK - CLIFFTON | BOTSWANA |
| 3 | 0:46.95 | OLESITSE - BENARD | BOTSWANA |
| 4 | 0:46.96 | SERIBE - OMPHILE | BOTSWANA |
| 5 | 0:47.04 | DIKGALE - RANTI | MASAI AC |
| 6 | 0:47.08 | MEKHISE - DITIRO | BACKTRACK AC |
| 7 | 0:47.18 | MASHIGO - KARABO | MASAI AC |
| 8 | 0:47.20 | OMAE - COLLINS | KENYA |
| 9 | 0:47.71 | PIENAAR - LEON | TUKS AC |
| 10 | 0:47.72 | NDONGENI - LIKHO | MASAI AC |
| 11 | 0:47.83 | SEELIGER - JAMES | TUKS AC |
| 12 | 0:47.88 | MOTONA - TSOANE | BOTSWANA |
| 13 | 0:48.17 | KHALANE - SAMUEL | LESOTHO |
| 14 | 0:48.20 | DU PREEZ - MARTHINUS | TUKS AC |
| 15 | 0:48.36 | PHOLO - MOTHUSI | BOTSWANA |
| 16 | 0:48.49 | NYAMBI - MBUSO | UNIVERSITY OF JOHANESSBURG |
| 17 | 0:48.75 | MATLATLA - THATO | TUKS AC |
| 18 | 0:49.13 | BRIEL - DANIEL | NYLSTROOM HS |
| 19 | 0:49.14 | MOTLOBA - KAMOGELO | ARB |
| 20 | 0:49.69 | ZAKWE - BONGANI | MASAI AC |
| 21 | 0:51.23 | MATSEKANE - KATLEHO | MASAI AC |
| 22 | 0:51.37 | SMIT - JACO | ACHILLES AC |