The proposed renewal of Trident nuclear weapons has prompted a rowdy and often ill-tempered debate at Holyrood.
Faslane is home to the Trident submarine fleet
SNP deputy leader Nicola Sturgeon urged politicians to "speak up for common sense" and vote for a motion opposing renewal of the system.
Labour said the SNP was simply using the issue to make a political point.
Despite securing the vote of Labour minister Malcolm Chisholm, the SNP's motion was defeated by 72 to 45 as MSPs failed to agree a position.
There were shouts of "shame" from the public gallery after the vote was announced.
Three amendments, which had been lodged by Labour, the Liberal Democrats and the Conservatives, were also defeated.
Mr Chisholm, the communities minister, has already spoken out against the UK Government's plans to replace the fleet of nuclear submarines, based at Faslane on the Clyde.
He was one of four Labour rebels, being joined by Bill Butler, Elaine Smith and Marlyn Glenn.
Ms Sturgeon opened the debate by calling the missile system "morally indefensible" and said replacing it would make the world a "more dangerous place".
She pointed out that eight countries in the world have nuclear weapons, while 180 do not.
Ms Sturgeon said: "Being nuclear free is the international norm and we should be striving to make it even more so and to make Scotland normal in that regard.
"This is our chance as a parliament to speak up for common sense.
"If we don't speak out now we will pay a heavy price for it - £25bn is a conservative estimate of the financial cost.
"I for one would rather see that money spent on health, education, pensions and on ensuring decent conditions and equipment for our conventional forces who have been so badly let down by this government."
Nicola Sturgeon urged her fellow MSPs to back the motion
The first Labour MSP to speak, backbencher Maureen Macmillan, said she opposed nuclear weapons.
However, the representative for the Highlands and Islands stressed that the decision on whether or not to replace Trident would be made by Westminster and not Holyrood.
She said: "It is the UK Government which will make the decision on Trident in due course and Scotland is ably represented by MPs who will take part in that decision."
Ms Macmillan added: "We have to use this opportunity to engage internationally with other nuclear powers at every level to bring about a reduction in nuclear weapons."
Tory MSP Phil Gallie warned against abandoning a "very successful nuclear deterrent".
The South of Scotland MSP said he was not defending Prime Minister Tony Blair's position, but told Ms Sturgeon that he could remember her party colleagues lobbying to save the nuclear submarines at Rosyth dockyards.
"I believe it was a flawed decision taken by a Conservative government at that time, but the SNP were out in force trying to retain those nuclear submarines at Rosyth.
"On that basis at one end of the argument there is a degree of hypocrisy," he said.
Former deputy first minister Jim Wallace said the Liberal Democrats did not want to rush into a decision on the issue and that the prime minister's public commitment to a new Trident system undermined his call for a full public debate.
Green MSP Chris Ballance described nuclear weapons as the "supreme conscience issue" which transcended party politics.
He said that even if MPs at Westminster voted in favour of a new Trident system, the campaign against it would continue.
The South of Scotland MSP said the world could move to disarmament and policing nations to ensure they do not acquire nuclear weapons.
"The other future sees more and more nations going nuclear, until an accident or a dictator starts a disastrous nuclear war," he added.
Scottish Socialist Party leader Colin Fox said the majority of Scots were opposed to nuclear weapons.
Jim Wallace said he did not want to rush into a decision
"They believe Scotland will be less safe as a consequence and I believe that an independent Scotland will scrap Trident.
"Just as an independent Scotland would not send Scottish troops to fight an illegal war in Iraq," the Lothians MSP said.
Labour's Jackie Baillie said that the Faslane base, in her Dumbarton constituency, provided 11,000 jobs in the local economy.
She said that she would ideally like to see a world free of nuclear weapons, but only as part of a multilateral approach where other nuclear powers also disarm.