The SNP donor issued a personal statement following interpretations of a risk management warning issued by his company, Stagecoach Group, on the independence referendum.
Stagecoach advised investors that changes to the regulatory environment or the availability of public funding as a result of the referendum, or from the subsequent UK general election, "could affect the group's prospects" in its preliminary results yesterday.
Better Together said Stagecoach drove "a coach and horses through the nationalists' case for separation", the Conservatives saw the threat of "a one-way ticket to a poorer nation" and the Liberal Democrats said the risk warning was an attempt to prevent shareholders being "thrown under the bus".
But Sir Brian said it was an advisory of the potential for political change to impact the business, both from the referendum and the 2015 general election, without commenting on "any particular outcome of either vote".
In the personal statement released today, Sir Brian said: "The preliminary results highlight to shareholders all areas where political changes could impact the business.
"The section which mentions the UK general election and Scottish referendum does not relate to any particular outcome of either vote.
"As a company Stagecoach remains neutral on the issue of Scottish independence, as it always has been.
"I personally hold the view that independence will create a positive outcome for all companies in Scotland.
"We have a once-in-a-generation opportunity to apply the levers of independence to boost jobs, enterprise and create a vibrant private sector alongside a more caring society - which should always go hand-in-hand. That is why I will be voting Yes on September 18."
Sir Brian has pledged to gift up to £1 million to the SNP by matching pound-for-pound every donation received during the year of the independence referendum.
He has also donated £100,000 to Yes Scotland-supporting group Christians For Yes.
He donated £500,000 to fund the party's 2007 election campaign and match-funded a further £500,000 ahead of the SNP's landslide 2011 win.