The apology came as Browne and McCain's Republican camp agreed on a settlement to the lawsuit that the singer filed in August, soon after the advertisement aired.
"We apologize that a portion of the Jackson Browne song 'Running on Empty' was used without permission," McCain, the Republican National Committee and the Ohio Republican Party said in a statement.
The Republican camp also pledged in future elections to obtain permissions and licenses from artists "where appropriate" when using their copyrighted works.
Browne, a liberal activist, told Billboard he would "absolutely" sue political candidates and groups he supports if they used his music without authorization.
"I really hope that people begin to understand what goes into making music," Browne told the music publication's website. "It's not just that one gets paid; it's that one's entire enterprise is fed, whether it's recording studios or the amount of money you can pay our band. ... It is a huge industry."
Browne had sued McCain, the Republican National Committee and the Ohio Republican Party, accusing them of copyright infringement.
It is not the first time a popular singer has gone after the Republicans for use of a song. In the mid-1980s, Bruce Springsteen complained about then-President Ronald Reagan's contextually inaccurate use of his song "Born In the U.S.A." during his re-election campaign.
(Reporting by Alex Dobuzinskis; Editing by Bob Tourtellotte and Peter Cooney)
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