Activists in Brighton voted in favour of a motion tabled by the Unite union to make their support for strikes conditional on UN backing.
The vote is not binding on MPs but Jeremy Corbyn has said the party must heed the opinion of members.
It follows calls from a senior Labour figure for a free vote in Parliament.
Shadow Chancellor John McDonnell told a meeting hosted by The Guardian at the Labour conference that Syria and the renewal of Trident were issues on which he did not expect consensus within the party and he believed a vote on military action in Syria should be made "on the basis of conscience".
The government was defeated in 2013 in a parliamentary vote on military action in Syria, but ministers have since said the case for UK intervention in the country should be made again.
In 2014 MPs voted in favour of RAF air strikes against Islamic State militants in Iraq.
Labour's new leader Jeremy Corbyn has called for a UN security council resolution and a fresh diplomatic push to end the violence in Syria.
The Labour conference will also consider an emergency motion, tabled by the union Unite, opposing the extension of the RAF's campaign against IS into Syria without "clear and unambiguous" authorisation from the UN.
But Mr McDonnell told a meeting on the fringe of the conference that many MPs did not back the leader's stance and said it may be necessary for them to "agree that we can't agree" - though he said that efforts to reach a consensus within the party were still ongoing.
Mr McDonnell said: "When you are sending people to potential loss of life, I think it is a conscience decision. It is a moral decision.
"On Syria, my view is it should be a free vote on the basis of conscience."
Prime Minister David Cameron has indicated he would like to extend the RAF airstrikes against the Islamic State group into Syria and could gain parliamentary backing from rebel Labour MPs, even if the party's leadership refuses to offer its support.
Mr Corbyn set out his views on Syria during his conference speech on Tuesday, saying that "the answer to this complex and tragic conflict can't simply be found in a few more bombs".
He added: "I believe the UN can yet bring about a process that leads to an end to the violence in Syria."
Meanwhile, the defeated Labour leadership contender Andy Burnham is to offer a tougher line on EU immigration during his speech on the final day of the conference.
Mr Burnham is to say that rules around the free movement of people in the EU are "widening inequality" and measures are needed to prevent the undercutting of wages by migrant workers.
In a speech aimed in part to win back voters from UKIP, the shadow home secretary will say the EU must provide a "floor beneath all workers" and protect the "going rate" on pay.
Mr Burnham, who was appointed shadow home secretary after he was heavily defeated by Mr Corbyn in the leadership race, will say that Labour had not "faced up" to some of the impacts of EU migration and consequently appeared "out of touch".
He will say: "To win back the voters we lost to UKIP I want to reframe the debate about immigration and the way Labour approaches it.
"For too long we have argued that free movement across Europe benefits everyone and affects all areas equally. That's just not true.
"In places, a free market in labour benefits private companies more than people and communities.
"Labour hasn't faced up to that and that's why we look out of touch."
Labour members have voted to oppose airstrikes against Islamic State militants in Syria, without a mandate from the United Nations.