Chiefs needed extra-time goals from Daniel Cardoso, Philani Zulu and Khama Billiat to advance to the quarter-final stages.
In the previous round, Middendorp's troops were also taken to extra-time by fellow third tier side Tornado FC.
“First of all it is our obligation to work it out and qualify for the last eight. Compliment to the spirit of the opponent to fight until the last second to work hard defensively,” the German tactician said on SuperSport TV.
“Of course we made it difficult for ourselves, I don’t want to comment on the execution of certain opportunities. I think during the first half and in particular the second half there were moments where we should have scored to make it an easier 90 minutes. In the end we have qualified and I’m very happy about it.”
Middendorp went on to say that he was reluctant to publicly comment about the chances missed in regulation time.
“You will not get any comment I will make in front of a camera talking about certain players that they have not scored or they did not use the chances. I think that should not be done. We will internally... if it is needed, I personally don’t need it, it’s in my memory, in my mental muscles I which moments you’re talking about.
“But it is like this. Sometimes strikers, defenders you can name them there is a run [where] it doesn’t work out. We’re not scoring at a certain time, good it is not for somebody to be blamed. It’s just a team effort at the end of the day and we have qualified, that’s it.
“From the dominance... our biggest opponent was in our own team, we can describe it and talk about it but I think everybody knows what I mean,” he said.