The board had recently approved the release of 70-year-old Bruce Davis but left the final decision to the governor.
Brown gave his decision to The Associated Press at the downtown Los Angeles County courthouse after a meeting with District Attorney Jackie Lacey.
"I find the evidence ... shows why he currently poses a danger to society if released from prison. Therefore, I reverse the decision to parole Mr. Davis," the written decision said.
Davis would have been only the second Manson-related murder defendant to be granted parole since Manson's killing spree began in 1969.
Davis was not involved in the notorious Sharon Tate-LaBianca killings but was convicted with Manson and others in the murders of a musician and a stuntman.
Steve Grogan, another participant in those murders, was released many years ago after he agreed to lead police to where the bodies were buried on a remote movie ranch in the San Fernando Valley.
Davis was 30 when he was sentenced to life in prison in 1972 in the case that was a postscript to Manson's notorious reign as leader of the murderous communal cult known as the Manson family.
Davis long maintained that he was a bystander in the killings of the two men, but in recent years, he has acknowledged his shared responsibility
Davis became a born-again Christian in prison and ministered to other inmates, married a woman he met through the prison ministry, and has a grown daughter. The couple recently divorced.
Davis also earned a master's degree and a doctorate in philosophy of religion.
Manson and three of his followers, Leslie Van Houten, Patricia Krenwinkel and Charles "Tex" Watson, remain in prison for life in the Tate killings. Their co-defendant, Susan Atkins, died of cancer behind bars in 2009.