Dandre Martin, 26, has been charged with assault and illegal firearm possession, police said on Monday.
Multiple people are believed to have opened fire in the busy downtown area, close to the state Capitol building.
Officials have identified the three men and three women killed in this year’s worst US mass shooting so far.
Three of the victims were men: Sergio Harris, 38, De’Vazia Turner, 29, and Joshua Hoye-Lucchesi, 32.
Three women were also shot dead: Johntaya Alexander, 21, Melinda Davis, 57, and Yamile Martinez-Andrade, 21.
Police say all six victims died at the scene, when multiple shooters opened fire just after 02:00 (09:00 GMT) on Sunday near the junction of 10th and K Street.
An additional twelve people were wounded in the shooting and taken to local hospitals. By Monday, seven had been discharged.
The violence was “unprecedented” for the city, its police chief said.
Police have executed several search warrants as of Monday. At least one handgun, now understood to be stolen, was recovered.
The family of Sergio Harris told local media the vivacious and friendly father had gone to a nightclub, London, late on Saturday and never returned.
Mr Harris’s wife, Leticia Fields, told the San Francisco Chronicle a stranger had told her on the phone that he had been shot.
“It sounds like a lot of innocent people lost their lives tonight,” Ms Fields told the Chronicle. “I’m taking it day by day. I haven’t told our 11-year-old yet”.
Mr Harris had gone to the nightclub with his cousin, DeVazia Turner – another of the victims – Mr Turner’s father told local TV station Fox40.
“There’s just nothing to say. I’m just here. I’m grief, that’s all – grief,” the elder Mr Turner said.
Videos posted online appear to show a brawl break out in the area – packed with restaurants and bars – in the early hours on Sunday, just before rapid gun fire sent people fleeing.
It was so far unclear whether the fight led to the shooting, police say, and on Monday, officials set up an online portal to ask the public to submit information from the scene.
In a statement on Sunday, President Joe Biden decried “another” instance of gun violence leaving “families forever changed. Survivors left to heal wounds both visible and invisible”.
Firearms are involved in approximately 40,000 deaths a year in the US, including suicides, according to the Gun Violence Archive website.
