Before the start of the game, City were forced into a change after Nana Akosah-Bempah pulled out and was replaced by Judas Moseamedi.
Keen to build on their first-leg lead, the Citizens started slowly but grew stronger as the half went by.
Putting out an experienced side perhaps highlighted their intentions to completely kill off the contest in the Mother City.
Following a dominant opening half, Benni McCarthy’s side went into the half-time breaking still carrying the one-goal lead from the first leg.
Chances by Moseamedi, Surprise Ralani and Shaun Roberts were, disappointingly, wasted in front of goa.
They made their second change soon after the restart as Craig Martin replaced Sibusiso Masina.
With the visitors providing few problems, the Citizens eventually went in front after Ralani curled in from the right side in the 56th minute to extend their aggregate lead.
After breaking the ice, Ralani made way for Thabo Nodada towards the midway point, as they were firmly in control of proceedings.
With game closing out, City kept their foot on the accelerator to book a spot in the first round proper.
Cape Town City: Walters, Kobola, Gumede, Fielies, Seedat, Johannes (c), Kewuti, Roberts, Ralani (Nodada 69'), Masina (Martin 46'), Moseamedi (Akosah-Bempah 69').
Subs: Stephens, Edmilson, Mkhize, Nodada, Martin, Lakay, Nana.
Buffaloes: Gwebu, Dlamini (Mhlanga 79'), Gamedze, Tsabedze, Mtseftwa, S. Mkhwanazi, Mazibuko, Mkhonta, Mazibuko, Maseko, Ngwenya.
Subs: Mkhwanazi, N.Dlamini, Mkhabela, S. Mkhwanazi, Mhlanga, M.Dlamini.