The broadcaster, which has been under increasing pressure to quit after several high-profile organisations did so, said it would suspend its membership for as long as the CBI was a registered supporter of the campaign.
A BBC statement said: "In order to protect the BBC's neutrality, the CBI and the BBC have agreed to suspend the BBC's membership during the business group's registration period under the terms of the Scottish Independence Referendum Act 2013."
The move came after pro-independence backer, Business for Scotland, questioned why the BBC had not resigned. The business network group, which campaigned for the CBI to declare its pro-UK support, has also claimed that all neutral members of the CBI can no longer remain with the organisation.
Chairman Tony Banks said: "It is now clearly not sustainable for any neutral member with a Scottish interest to remain in the CBI by the end of this week. The legal position is clear.
"All members of the CBI, anywhere in the UK and particularly if they receive public funding, should now be seen to ask serious questions even if we already know the answers."
The CBI said any member leaving was cause for regret but believes it has a man-date from the majority of its members.