Five days after slipping to a horror upset 1-0 loss to Bahrain on the Gold Coast, Graham Arnold's chances were unable to manufacture a winner against the world's No.133-ranked team.
Australia had the weight of possession, 12 shots and 15 corners, but were left to rue their inability to break open Indonesia's hard-working defence - who they beat 4-0 in January's Asian Cup.
The Socceroos have just one point from two games they were expected to win in the third round of qualifying, piling pressure on Arnold and his charges.
Needing a top-two spot to qualify directly, the winless Socceroos (0-1-1) sit fifth in group C, with Saudi Arabia beating China 2-1 on Tuesday night.
Arnold had wanted Australia to be braver and more creative in attack, and he adjusted his starting line-up at Gelora Bung Karno Stadium in Jakarta.
Australia's Nestory Irankunda (l) endured a frustrating night in Jakarta including hitting the post. (AP PHOTO)
Nestory Irankunda headlined five changes as a secondary striker alongside Mitch Duke, who replaced the suspended Kusini Yengi, with Arnold hoping to get him in behind and one-on-one with defenders.
Irankunda rifled a scintillating long-range shot off the post in the 34th minute, and was a clear bright spark alongside right-back Alessandro Circati.
Samuel Silvera was recalled on the right wing while Keanu Baccus returned from injury in midfield, replacing Connor Metcalfe (injured), and Cam Burgess came in for Kye Rowles.
Mat Ryan was forced into a double save inside the opening 20 seconds while Ragnar Oratmangoen got in behind Australia's defence within the first couple of minutes.
But the Socceroos weathered the early storm and took control.
Indonesia's defence scrambled after an Australian corner in the 21st minute, with a Circati volley blocked before goalkeeper Maarten Paes saved a powerful Harry Souttar strike.
Souttar forced a Paes save with a header shortly after as Australia piled on the pressure.
Irankunda's 34th minute strike somehow rebounded off Paes's back to safety and a minute later, Craig Goodwin smacked a close-range effort into the Indonesia goalkeeper.
Despite Australia's weight of chances, Indonesia's under-siege defence held firm through to half-time, then quelled the Socceroos' attack after the break.
Arnold turned to Awer Mabil, Adam Taggart and Josh Nisbet to attempt to create an opening.
Taggart almost created a goal straight away, but fired straight at Paes, while Mabil turned a header wide in the 78th minute.
The Socceroos are next in action against China in Adelaide on October 10, then against Japan in Saitama five days later.
