First Minister Alex Salmond announced his resignation after the result, in which 55 per cent of voters said "No" to breaking away from the United Kingdom, and has now been replaced by his deputy Nicola Sturgeon.
Delegates rubber-stamped Sturgeon's election as SNP leader at the party's annual conference in Perth - she was the only candidate - paving the way for her appointment as Scotland's first female first minister next week.
Salmond led the SNP for nearly 20 years and spent seven as first minister, transforming the nationalist party from a marginal organisation to a major political force.
In his outgoing speech to the conference later today, Salmond will repeat his belief that Scotland can still become an independent nation despite the referendum vote.
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"When the history of Scottish independence is written, be in no doubt that the 18th September 2014 will be remembered as the most significant breakthrough in Scottish political history," he will say.
"A much higher number than our opponents ever thought possible when we started this campaign."
The SNP's membership has swelled since the referendum from 25,000 to 84,000, and Salmond said he hoped it could reach 100,000 before the British general election in May.
Although Scotland remains part of the UK, the closeness of the referendum campaign prompted the British government to promise new powers for the devolved government in Edinburgh.
Welcoming her appointment, Sturgeon said it was a "good time for our a party and it's a good time for our country".
The conference also saw Stewart Hosie elected as the party's new deputy leader.
He is a lawmaker in the British parliament in London but not the Scottish parliament, so will not be able to take over Sturgeon's job as deputy first minister in Edinburgh.