Tom Rogic’s injury-time thunderbolt settled an Asian Cup thriller on Tuesday as defending champions Australia beat Syria 3-2 to reach the last 16 and knock out their war-torn rivals.

The result meant the holders finished second in Group B behind Jordan, whose simultaneous 0-0 draw with Palestine gave the latter hope of qualifying as one of the best third-placed teams.

Syria, vocally backed by thousands of their fans in Al Ain, twice fought back from a goal behind before Rogic slammed home the winner in the third minute of injury time.

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Injury-hit Australia, with only six outfield players on the bench, needed just a draw to go through and they got there – but there were twists along the way. “It was a helter-skelter game at times,” said Socceroos coach Graham Arnold.

“On another night we could’ve scored more goals but it was a great learning process for our young players. It was a good performance just in terms of the grit and determination.”

Syria looked an early threat before Australia started to get a grip on the game and Hibernian striker Jamie Maclaren flashed a header just wide. There was drama on the half-hour when a Syrian free-kick bounced through a packed penalty area and into the net, but the goal was ruled out for a foul on Mark Milligan.

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But Australia were getting close and Awer Mabil, after seeing one raking shot blocked, unleashed a fabulous effort which curled into the top corner four minutes before half-time.

However, the lead lasted just two minutes as Mouaiad Alajaan’s cross picked out birthday boy Omar Khrbin, turning 25 on Tuesday, who saw his header saved by Brighton’s Mathew Ryan but then gobbled up the rebound.

On 54 minutes, there was controversy when Chris Ikonomidis’s shot was hooked away by Omar Al Midani – but the ball was judged to have crossed the line by the additional assistant referee, who was surrounded by Syrian players.

Syria penalty

The incident silenced the massed ranks of Syrian fans but there was uproar around the stadium shortly afterwards when their team vehemently claimed a penalty for a Milligan handball.

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Australia looked firmly in control and they could have had a third goal when substitute Apostolos Giannou saw a low shot cannon off the base of the upright. But Mexican referee Cesar Ramos threw Syria a lifeline when he gave them a penalty after Omar Al Soma went down in the box – and the striker stroked them level once more with 10 minutes to go.

It looked like Syria would escape with a vital point before Celtic’s Rogic, playing the tournament with a broken hand, belted Australia’s third from distance. “Fitness was the critical factor,” shrugged Syria’s interim coach Fajr Ibrahim, who took charge when Bernd Stange was sacked following their defeat by Jordan.

“There wasn’t a big difference apart from the fitness of the Australian team. They were superior.”

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Meanwhile in Dubai, Jordan were held to a goalless draw by Palestine in a fiery clash to preserve their unbeaten record and progress as Group B winners. Twice quarter-finalists, in 2004 and 2011, Jordan stunned holders Australia in their opening game before beating Syria 2-0. But they found plucky Palestine a tougher nut to crack in Abu Dhabi.

Abdallatif Al Bahdari’s header gave Jordan a scare on the hour-mark of a match that was not one for football purists. Jordan went close when Ahmad Ersan’s long-range blast was blocked by Palestine goalkeeper Rami Hamada before the game petered out with both sides content to take a draw.