Napolitano disputed findings that her office hid $175 million and said much of the money is committed to systemwide university programs, leaving a much smaller amount -- about $38 million -- in reserve for unexpected expenses.
Still, she and the board have committed to implementing the audit's 33 recommendations to improve transparency and spell out policy.
Protesters disrupted the UC regents meeting on Wednesday, saying UC should have avoided a tuition hike if the Office of the President had extra money stashed away.
The audit drew bipartisan legislative ire and prompted Gov. Jerry Brown to withhold $50 million from the UC system's budget to "hold their feet to the fire."
Some board members complained about poor press coverage, and thanked the auditor for clarifying that the president's office did not commit malfeasance.
"I was delighted when I found out we had the possibility of Janet Napolitano as our president. I'm still delighted. She has a record of being someone of great character who is visionary and gets things done," said Regent Norman J. Pattiz to Howle.
"I think, frankly, you lucked out that the president agreed to all of them."
Howle also criticized the president's office for intentionally interfering with the audit by screening survey responses of individual campuses. Napolitano has apologized for the way her office handled the investigation.
The governing board of one of the most prestigious public university systems in the country also is scheduled to vote on a proposal to cap out-of-state undergraduate enrollment at 18 percent.
This is a touchy subject for a public university system that benefits from higher out-of-state tuition but hears complaints from California undergraduates who say they are being squeezed from coveted spots by wealthier nonresidents.
State lawmakers last year withheld $18.5 million unless the system adopted a cap.