Two quality strikes from outside the box proved the difference but it was the intervention of the VAR which "changed the game", Rudan said.
The Nix were already 2-0 down following goals in either half from marquees Ritchie De Laet and Bruno Fornaroli.
But when a shot by Mitch Nichols struck the arm of City skipper Scott Jamieson it looked like the Kiwi outfit could claw one back.
“We’re all clear, everybody else saw it, I think everybody in the stadium saw it was a handball,” the coach said post-match.
“It was just a matter of whether it was inside the box or not. I thought it was from where I was and then I turned around and got it confirmed by two people at Fox Sports.
"So when they went to the VAR I was super confident it was going to be a pen.”
It wasn’t. Jamieson’s arm was close to his chest at impact and referee Adam Fieldin,g after consulting with the VAR, signalled a drop ball on the edge of the area. Rudan, already carded earlier in the night, was gobsmacked.
“When you’re on a yellow card you’ve got to be very careful with what you say, but I just asked for an explanation and he just said it wasn’t a handball, they reversed the decision. (I) said, ‘who has’ – the VAR.”
Despite two losses on the trot, Rudan said he was pleased with the discipline of his side.
“Say what you want about the actual game plan but we were very disciplined,” he said.
“Could we have done better, yes, particularly with the ball. We gave the ball away a little bit too easy, too cheaply in the first half. We need to be better in that department as well.
“But we’re not going to be a side that’s going to out-possess teams. We want to frustrate them and we’re very early in our building blocks as well, in our development phase, very early.
“The first round it was good, in the second round it was good. That’ll be us. We’ll create opportunities and chances but we’ve just got to be better in certain moments.”