Milligan scored a goal in each half, including the winner in the 78th minute. Kristian Sarkies scored the other goal for Australia, while former Sydney FC striker Jeremy Brockie scored both goals for New Zealand.
Qantas Under 23s Head Coach Graham Arnold was happy with result but knows there is still work to work to be done.
"We have been working a lot on our combination play and I was very pleased with our performance in stages," he said.
"If anything I was a little disappointed that we didn't get on the end of things. We should be able to kill those games off earlier.
"At the moment I'd say that we are around 75% fitness levels and over the next three and half weeks we want to increase that by another 20-25% to peak in China.
"We do need to work on our defence. The first goal came from a set move so we need to improve on that.
"But overall we played some good football and now we are looking towards the opening match of the Olympic Games against Serbia on the 7th of August," concluded Arnold.