The Socceroos never really hit top gear, but quick thinking and a neat finish from Milligan four minutes before half-time was enough to see the hosts book their ticket to Qatar - much to the delight of the 20,422-strong crowd.
Milligan, deployed as a central defender for the match, used his shoulder to deflect a looping dead-ball strike from Luke Wilkshire onto the crossbar and then pounced on the rebound with Indonesia goalkeeper Markus Rihihina stranded.
Wilkshire then delivered pinpoint service from a corner at the end of the first half, but Rihihina met Simon Colosimo's powerful header with an amazing leaping one-handed palm over the bar to keep his side within reach at the interval.
The hosts clicked into gear after half-time, but found it tricky to make a further impact on the scoreboard despite the numerous entries into the box.
Giant striker Josh Kennedy, anointed as the man who could be the difference by both camps at the pre-match press conference, went close with a pair of headers after being starved of the ball in the first half.
Jason Culina, who was given the captain's armband and much more freedom to roam forward than he is usually accustomed to, looked to take matters into his own hands, but a series of long-range attempts failed to find the back of the net.
In the end it mattered little. After a trying qualification campaign, typified by a loss to Kuwait on home soil last year, Australia needed to take at least one point away from the final Asian Cup qualifier to ensure they would not miss out.
National coach Pim Verbeek handed full debuts to both Tommy Oar and Shannon Cole, and entrusted a squad made up of predominately A-League talent to get the job done against Indonesia, ranked 136th in the world.
Verbeek would have had a few nervous moments while his side failed to score in the first 40 minutes despite controlling the tempo and dominating possession in the early stages of what was a reasonably physical encounter.
But Milligan's impressive effort allowed Verbeek to collect his thoughts before a thoroughly entertaining second period where Oar's slick skills came to the fore.
The 18-year-old winger was kept reasonably quiet in the opening half, but his pace and lethal left foot were more often than not a part of Australia's surges forward after the break.