| Place | Performance | Athlete | Team |
| 1 | 03:56.03 | Q: DOMINGO - KEANU | NORTHWEST UNIV POTCHEFSTROOM A |
| 2 | 03:58.50 | Q: NDIMANDE - NTUTHUKO | UNIVERSITY OF JOHANNESBURG B |
| 3 | 03:58.66 | Q: REES - GARRICK | UNIVERSITY OF PRETORIA A |
| 4 | 03:58.75 | Q: MPHAHLELE - RYAN | UNIVERSITY OF JOHANNESBURG A |
| 5 | 03:59.78 | Q: MBATHA - SIYABONGA | VAAL UNIV OF TECHNOLOGY |
| 6 | 04:01.66 | q: NWAGU - TSHEGOFATSO | UNIVERSITY OF JOHANNESBURG A |
| 7 | 04:09.83 | q: JALI - THEO | UNIVERSITY OF WESTERN CAPE A |
| 8 | 04:16.66 | -: MNASE - SIYABULELA | UNIVERSITY OF FORT HARE |
| 9 | 04:20.03 | -: MASHAPU - THABISO | TSHWANE UNIV OF TECHNOLOGY |
| 10 | 04:27.98 | -: MOTLOUNG - DUMISANI | UNIVERSITY OF FREE STATE A |
| 11 | 04:32.47 | -: TLOU - PHATHUTSHEDZO | NELSON MANDELA UNIVERSITY |
| 12 | 04:34.60 | -: GULE - MFUNGELWA | UNIVERSITY OF MPUMALANGA |
| 13 | 04:35.58 | -: BOOYSEN - CURTIS | UNIVERSITY OF WESTERN CAPE B |
| 14 | 04:45.37 | -: MOSTERT - NIELBERT | UNIVERSITY OF FREE STATE B |
| 15 | 04:57.25 | -: KOK - SHALTON | CENTRAL UNIV OF TECH BFN |
| 16 | 05:08.61 | -: BHIXI - THABISO | UNIVERSITY OF FORT HARE |