He rejected the legislation Friday because he says it would cause more drunken driving.
California lets bars serve alcohol until 2 a.m. Brown says the bill would have added two hours of early morning "mayhem."
The state Legislature approved the bill in August.
The five-year pilot program would have allowed extended hours in nine California cities.
In Southern California, those cities included Los Angeles, Long Beach, West Hollywood, Palm Springs, Cathedral City and Coachella. The other cities were Oakland, Sacramento and San Francisco.
The bill was opposed by anti-drunk driving activists.
If the governor had signed the bill into law, it would have taken effect in 2021.
The Associated Press contributed to this report.