Australia were already guaranteed to reach the round of 16 but needed a win or draw at Doha's Al Janoub Stadium to finish top of group B.
Martin Boyle's spot-kick in the opening minute of first-half injury time, after a dubious handball call on Odiljon Hamrobekov following a VAR review, gave Australia the ascendancy.
But Uzbekistan seized control after the break and equalised when Azizbek Turgunboev leapt over Aziz Behich and headed home in the 78th minute.
Azizbek Turgunboev climbs above Aziz Behich to head Uzbekistan's equaliser at Al Janoub Stadium. (AP PHOTO)
It was Uzbekistan's first goal against Australia in five meetings and ended a run of six consecutive clean sheets for the Socceroos.Â
Uzbekistan finished second on five points, while Syria beat India 1-0 to finish third on four points, sealing progression as one of the best third-placed finishers while knocking out both India and China, who came third in Group A but cannot now progress.
The Socceroos will play the best third-placed team from either group C or D, and will likely be on the opposite side of the draw to tournament favourites Japan.
Australia's coach Graham Arnold watches the Socceroos draw in Doha, giving him much to ponder. (AP PHOTO)
But there is plenty for Arnold to address, with Australia's struggles to break down a defence, lack of creativity and a second-half fadeout among the concerns.
Kusini Yengi replaced injured striker Mitch Duke (hamstring) among five changes, while attacker Riley McGree made his first start of the tournament.
Harry Souttar had hearts in mouths in the ninth minute when he turned the ball over to Oston Urunov, then recovered to make the crucial tackle.
Yengi headed home in the 11th minute but Martin Boyle was offside in the build-up.
Australia should have scored in the 42nd minute when Yengi went on a wonderful weaving run through Uzbekistan's defence and cut the ball back for McGree, who inexplicably shot wide.
But luck was in Australia's favour.
During Yengi's run, he attempted to get past Hamrobekov and the ball flicked off the defender's arm, which he was using to brace his fall, then back into the striker's path.
After a lengthy VAR review, Hamrobekov was penalised and booked and Boyle drilled the penalty into the bottom corner.
Uzbekistan's Umar Eshmurodov headed home in the 60th minute but was offside.
It proved a warning shot.
Eighteen minutes later, Turgunboev brilliantly buried a wonderful dipping cross from Jaloliddin Masharipov to ensure Uzbekistan's progression.
5°C