The failed motion to suspend standing orders was moved by the Greens, whose leader Richard Di Natale said that leaving the decision on air strikes to the Prime Minister is a "very dangerous situation".
Liberal Senator Eric Abetz said the argument put forward by the Greens was "completely devoid of any substance".
"Sometimes, regrettably, evil has to be fought with force," he said.
The motion to suspend standing orders was defeated by Liberal and Labor Senators, 10 votes to 37.
The call for debate followed an announcement that Australia has agreed to a US request to extend airstrike operations to Islamic State targets in Syria.
Prime Minister Tony Abbott made the announcement in Canberra on Wednesday after cabinet signed off its approval.
"There can be no stability and no end to the persecution and suffering in the Middle East until the Daesh death cult is degraded and ultimately destroyed," he told reporters.
Daesh could not be defeated in Iraq without being defeated in Syria, Mr Abbott said.
He emphasized Australian aircraft would be targeting Daesh and not the Assad regime, "evil though it is."
Australia will be joined by other coalition partners including the US, Canada, Turkey and some Arab nations.
Defence minister Kevin Andrews sais RAAF flights over Syria were a practical and logical extension of the existing operation.
"It's quite clearly in Australia's national interest," he told reporters.
The decision reflected the government's "steadfast committment" to degrade, destroy and defeat Daesh.
But independent MP Andrew Wilkie characterised the decision to take part in Syrian air strikes as "a chest-thumping exercise for political gain".
Mr Wilkie told reporters that the Australian contribution would make little difference, stating instead that it was "a very bad decision and a very reckless and dangerous decision".
"Us joining in the bombing of Syria, effectively an invasion from the air, will be illegal," he said.
"It seems that this government has learned absolutely nothing from history. We shouldn't have gone there in the first place."
