A temporary suspension was declared on Tuesday after Russia warned it would treat aircraft from the US-led coalition as potential targets.
That warning came after the US shot down a Syrian military plane.
The Australian Defence Force said it had been "a precautionary measure to allow the coalition to assess the operational risk".
The statement did not say how long the suspension had been in place.
Australia has deployed about 780 military personnel as part of the US-led coalition fighting the so-called Islamic State (IS) in both Iraq and Syria.
The temporary halt in operations came as the coalition and the fighters it is supporting on the ground attempt to oust IS militants from Raqqa, the de facto capital of the "caliphate" they proclaimed in 2014.
Australia joined the US-led coalition in Syria in September 2015, but did not carry out any operations in the country between March and May this year, according to the defence department.
Russia warned on Monday that it would track coalition aircraft with missile systems and military aircraft, but it stopped short of openly saying it would shoot them down.
The move came after the US shot down a Syrian Su-22 which, the Pentagon said, had bombed US-backed fighters battling IS near the town of Tabqa in Raqqa province.
It was believed to be the first air-to-air kill of a manned aircraft by a US military jet since the Kosovo campaign in 1999.
Australia has said it will resume its military air operations over Syria.