The killing took place on April 27 when Michael Earl-Wayne Anthony, the 33-year-old guard working for Walgreens, fatally shot alleged shoplifter Banko Brown.
A surveillance video, released on Monday, showed Anthony trying to stop Brown as he tries to leave the store with a bag of items before they engaged in a fight.
Brown appeared in the footage walking backward out of the store, and as he exited the store Anthony fired one shot into his chest.
San Francisco District Attorney said the guard acted in self-defense and there is no evidence to charge him with a crime.
"We do not believe there is sufficient evidence to overcome what we would expect his defense of self-defense to be," Brooke Jenkins told KTVU in an interview on Monday.
"[Anthony] has specifically articulated to the police, more than once, the facts surrounding the incident and explained that he believed he was in imminent danger, and at this time we don’t believe there is anything to overcome those statements."
The San Francisco Chronicle newspaper cited the guard claiming that Brown, who was unarmed, had threatened to “stab” him, in remarks that witnesses did not substantiate.
Brown later died from his gunshot wound and no weapon was found on his body, sparking anger among activists.
San Francisco police initially arrested Anthony, with the police chief saying, “You have to use force appropriately within the law.” But he was released days later.
The killing and Jenkins's announcement sparked protests on Monday, with people marching in San Francisco to demand justice for Brown.
San Francisco Supervisor Shamann Walton also criticized Jenkins on Monday, saying her decision "gives every armed security guard in San Francisco a license to have an open season to shoot and kill" Black people for alleged shoplifting.
Walton noted that "I have watched the video several times, Banko Brown was clearly walking backwards, after being thrown to the ground, punched, and abused by the security guard for several seconds."
Friends and family of Brown also said that Jenkins’ decision not to seek charges against the guard “sets a dangerous precedent”.
“It’s beyond comprehension why charges wouldn’t be filed,” John Hamasaki, who ran for district attorney last year and is a former member of the San Francisco police commission, said, adding “We see cases filed all the time when there’s a fight and somebody pulls out a gun and shoots. You don’t get to execute somebody once the threat is over, and that appears to be what’s happening.”
The video, he said, seemed to show the guard quickly escalating the situation.
“This is not what security guards are supposed to do. And it puts everyone in danger when they use excessive force at the beginning of an encounter.”
The case has again put racial discrimination in the US under scrutiny.
In recent years, police violence has assumed alarming proportions in the US, with people of color being the main targets.