The unofficial time of death was 12.35am local time (7.35pm AEDT) on Tuesday.
He was executed by lethal injection at San Quentin State Prison, north of San Francisco after the US Supreme Court and Californian governor Arnold Schwarzenegger denied appeals to spare his life.
The US' highest court refused to stay the Williams execution, but did not say why.
Governor Schwarzenegger refused to grant him clemency earlier in the day, saying his refusal to admit he killed the four victims was the reason.
Civil rights leader Reverend Jesse Jackson said he broke the news to Williams in jail.
"He said, don't cry, let's remain strong. He smiled ... with a certain strength, a certain resolve," Rev Jackson told Reuters.
Anti-death protests
Around 2,000 death penalty opponents gathered outside the prison gates, where Rev Jackson addressed the crowd.
Some even brought children.
"I wanted to show them we oppose the death penalty even if you are a murderer," said one protester, holding hands with her two young children and wearing a "Save Tookie" badge.
Williams co-founded the deadly Crips gang and was convicted of murder, however found redemption behind prison walls and since became an anti-crime activist.
The US federal appeals court rejected an application for a stay of execution on Monday, which claimed Williams should have been allowed to argue at his trial that someone else killed one of the four victims.
It was also claimed that questionable forensics had linked him to the other killings.
No justification for clemency
Governor Schwarzenegger said he studied the history and wrestled with the profound consequences but he could find no justification for granting clemency.
“The facts do not justify overturning the jury’s verdict or the decisions of the courts in this case,” the governor said.
“If Stanley Williams does not merit clemency… what meaning does clemency retain in this state?” asked defence lawyer Peter Fleming Jnr.
The last time that a California governor granted clemency was in 1967, when Ronald Reagan spared a mentally infirm killer.
Renounced violence
During his time on death row, Williams renounced gang violence and wrote books dissuading youths from joining gangs.
He has been nominated a number of times for the Nobel Peace Prize.
Williams also has attracted a number of high profile supporters, including Oscar-winning actor Jamie Foxx, rap star Snoop Dogg, Bianca Jagger and former M*A*S*H star Mike Farrell.
A film starring Academy Award winner Foxx was made about Williams.
Executions are relatively rare in California.
William's execution comes just over a week after a double murderer became the 1,000th prisoner to be executed in the US since capital punishment was reintroduced in 1976.