Jackson Irvine's cross forced an own goal from Elkan Baggott to give Australia the lead in the 12th minute, their earliest of the tournament in Sunday's clash.
Martin Boyle doubled Australia's lead, and took the wind out of Indonesia's sails, in the 45th minute with a terrific diving header.
Indonesia goalie Ernando Ari Sutaryadi is beaten by Martin Boyle's header that put Australia two up. (AP PHOTO)
Craig Goodwin returned from injury to add a third in the 89th and Harry Souttar buried another in injury-time for Australia's heaviest win of the tournament in front of 7863 fans at Jassim bin Hamad Stadium in Doha.
Despite the scoreline, there will be some concerns for coach Graham Arnold, though.
Realistically, only a lack of end product stopped Indonesia from scoring early, while Australia didn't have a shot until Boyle's goal and didn't record a second until the 80th minute.
With a pro-Indonesia crowd bringing a loud, parochial atmosphere, Australia's defence looked panicked.
Veteran striker Bruno Fornaroli replaced Kusini Yengi up top and started brightly but faded.
Just three minutes into the game, Indonesia's Rafael Struick flicked a close-range effort over the bar - one of five first-half shots from the world No.146.
Australia drew first blood when Irvine burst down the right and into the box, before his attempted cross took a heavy deflection off Baggott and beat goalkeeper Ernando Ari.
Australia relieved the pressure with one of their best goals in Doha.
Martin Boyle after scoring Australia's key second goal in their Asian Cup win over Indonesia. (AP PHOTO)
Keanu Baccus slipped a lovely reverse pass to Riley McGree, who fed the ball out wide to Gethin Jones.
The full-back launched a wonderful crossfield ball towards the far post, where Boyle flung himself forward to head home.
Indonesia faded in the second half as Mitch Duke (hamstring) and Goodwin (knee) returned from injury in the 61st and 86th minutes respectively.
Jones, who replaced Nathaniel Atkinson in the starting line-up, came off holding his groin in the 69th minute.
In the dying minutes, Australia broke through again when Irvine's header was brilliantly saved by Ari, only for Goodwin to pounce on the rebound and bury a skidding shot.
Two minutes later, from a free kick, Goodwin turned provider for Souttar, who turned home a lovely flick-header.
South Korea and Saudi Arabia play on Tuesday (3am Wednesday AEDT), with the quarter-final scheduled for Friday (2.30am Saturday AEDT).
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