Australia has missed a chance to take a decisive advantage into the home leg of its World Cup qualification play-off against Syria, succumbing to a late equaliser in a tough first leg in Malaysia.

Minutes from a hard-fought victory, the Socceroos fell foul of a contentious penalty decision when Mat Leckie contested a high cross with Syrian striker Omar Al Soma.

Though Leckie used no hands to boost his jump and won a clean header, the referee awarded a penalty for a nudge in the back of the lanky striker — Al Soma stepped up and ruthlessly slotted the penalty.

It was a bitter pill to swallow for Australia, who led 1-0 from Robbie Kruse's first-half opener and perhaps should have put the game to bed before the penalty decision.

Robbie Kruse opened the scoring for the Socceroos late in the first half. ( Reuters: Lai Seng Sin )

The goal came after Leckie himself drove to the byline and drove a shot at goal, but the strike needed the toe of an opportunistic Kruse to divert it into the back of the net.

The Socceroos controlled all of the first half and looked to settle the game after the break, most notably when Tomi Juric hit two consecutive shots against the same post to no avail.

But as Australia's chances slipped away, Syria gained confidence and began raiding the Socceroos' goalmouth.

Al Soma very nearly scored from a headed effort that struck Ryan's face en route to the post, one of many near misses for Syria in the second half.

Omar Al Soma was a constant handful for Australia, and slotted his late penalty. ( Reuters: Lai Seng Sin )

There was time for one last Australian chance, but Trent Sainsbury's goal-bound header was incredibly saved by Syrian keeper Ibrahim Almeh.

Once again, Australia's frustration comes from not making the most of its spells of dominance and allowing the opposition an avenue back into the game — despite Aaron Mooy's midfield dominance, none of his forward team-mates were able to make the most of his brilliant passing.

Syria's incredible story stays alive at least for one more game, but to break Australia's unbeaten run in Sydney would require some sort of fairytale.