The Socceroos escaped with a 0-0 draw in their opening match of the tournament against South Korea on Saturday, surviving a major siege on their goal by the home nation.
Seeking to make amends, they took the game to the Samurai Blue at Hwaseong Sports Complex, coming back from two goals down to level at 2-2, before giving away a late goal to end proceedings empty-handed.
However, Milligan felt his team-mates acquitted themselves well up against their regional rivals, validating the tactical decisions of head coach Holger Osieck.
"I thought we did well, especially in the second half," he said. "We played a slightly different game, especially in the pressing sense. We tried to press a lot higher.
"It came together a bit in the second half, we played some good football in patches and all the substitutes that came on I thought were outstanding tonight.
"It's been a tough couple of games for us physically and mentally. We dug deep in the second half, not just physically. We still tried to play a little bit without resorting to any silly stuff and we got our rewards for it.
"Unfortunately we got a little bit eager in conceding that third goal but there were a lot of positives to take from it."
Milligan's fellow midfielder Ruben Zadkovich also saw out the full 90 minutes in difficult conditions, saluting the effort of a team composed largely of players on the fringes of the national team.
"I felt the boys played quite well," he said.
"First half we were probably a little bit on the back foot, there wasn't much penetration. Holger corrected that at half-time, told us what we should be doing with our attacking tactics.
"It was a much improved performance on the Korea game against even more talented opposition. A little bit disappointing to get back to 2-2 and concede straight away."