Goals by Lerato Lamola, Zolani Nkomphelo and Nduduzo Sibiya clinched all three points for Abafana Bes’thende.
Lamola opened the scoring for the visitors after 33 minutes. However, the Durban side's lead lasted only five minutes, as Egyptian marksman Amr Gamal equalised with his first goal for the Clever Boys following his recent loan move from Al-Ahly.
After the break former Mbombela Stars attacking midfielder Nkomphelo put the KZN outfit back in front after a fantastic counter attack with a ferocious strike from outside the penalty area.
With Wits struggling for an equaliser, coach Gavin Hunt opted to introduce Eleazar Rodgers for Hellings Mhango in the 69th minute.
However, Sibiya put the game beyond doubt with a strike in the dying minutes as Arrows registered their first win of the season.
The result moved Clinton Larsen's charges up to sixth spot in the standings. Wits dropped to 14th place with a point from three league matches, adding to the misery of their MTN8 semi-final elimination at the hands of Cape Town City on the weekend.
Wits: Josephs, Hlatswayo, Damjanovic, Classen, Mhango (Rodgers 69'), Mlambo, Tlhone, Motshwari, Frosler, Ntshangase, Gamal Aml.
Arrows: Gumede, Dube, Mngwenge, Mzava, Nkombelo, Bilankulu, Jooste (Cele 60'), Shongwe, Mahachi, Magunbane, Lamola (Mutizwa 80').