The corporation told the campaign to remove its branding after it produced a leaflet warning the BBC would be "broken up" by independence. "Don't let them switch off our BBC... one of the best things about being in the UK," it said.
The leaflet also warned a Scottish Broadcasting Corporation, as recently floated by Alex Salmond, could mean higher licence fees, more adverts to fund the service, and no more access to the BBC's website or iPlayer service in Scotland.
Concerned voters were urged to send their details to Better Together on a form emblazoned with the official BBC logo. Electronic signatures suggest both documents were created by Better Together's chief executive, Blair MacDougall.
The BBC insists anyone using its branding must obtain "prior written consent" – and Better Together failed to get it. The corporation says that because it is politically neutral it would never allow its logo to be used in a way that could give the impression it endorsed one side of the independence debate.
SNP MSP Joan McAlpine said of Better Together: "They have been caught red-handed breaking the rules, and they must pulp these leaflets and apologise for trying to politicise the BBC."
A BBC spokeswoman said: "We have written to the campaign to request that they remove the logo from their materials."
Better Together said it would comply with the BBC request, but added that the SNP intervention had inspired it to print 100,000 copies of the leaflet minus the logo.