The regents approved an annual salary of $570,000 for Napolitano at a meeting disrupted by about 25 protesters who accused Napolitano of accelerating deportation of undocumented immigrants, the Los Angeles Times reported.
Napolitano will also receive free housing, an annual automobile expense of almost $9,000 and $142,500 for relocation costs, the newspaper said.
UC police removed at least five of the protesters from the meeting room.
Napolitano, 55, will be the first woman to head the university system in its 145-year history.
She has headed the Department of Homeland Security since being appointed by President Barack Obama in 2009 at the start of his first term. President Bill Clinton named her U.S. Attorney for Arizona in 2003, and she was subsequently elected governor of Arizona before joining Obama's Cabinet.