Amakhosi scored either side of half-time, through Pule Ekstein and Dumisani Zuma, to progress to the semi-finals of the last knockout competition for the season. They will face Chippa United in the last four, while Golden Arrows will take on National First Division outfit TS Galaxy in the other semi-final match.
Middendorp brought on Zuma for right back Ramahlwe Mphahlele at the start of the second half, changing the system they had in the first stanza.
"The change in the second-half...we had not done it to our satisfaction. We had holes on the left and on the right. I was hundred percent sure knowing the expertise of technical team side of Cape Town City," Middendorp said after the game.
"We had Khotso [Moleko] on the right and [Siphosakhe] Ntiya-Ntiya on the left, ja it was a bit like playing chess. It doesn't matter if you play Pirates in the league or Maritzburg in the league, or if you play Magic FC, Tornado FC, sometimes of course the planning is one part and the execution is another part. Of course it's reflecting what's going on only during the game and to react about it. Actually I think it was well executed from the players today."