Haftom Zarhum, a 29-year-old Eritrean who worked at the Beersheva central bus station, was shot by a security guard, then set upon by an angry mob who wrongly believed he had just shot a soldier at the scene.
Zarhum later died of his injuries, according to Israel's Southern District Attorney's office.
Video of the incident, which showed people angrily kicking Zarhum in the head and body and slamming him with a bench, was broadcast on television, sending shock waves through Israeli society.
The district attorney's office said in a statement that four people had been charged with causing grave bodily harm for their roles in last year's assault, which it described as a "lynching."
One of the men charged was a prison guard.
Victim was clearly 'helpless'
According to the indictment, an Arab Israeli gunman shot and killed an Israeli soldier at the station on October 18. In the chaos that ensued, the station's security chief misidentified Zarhum, who was crawling on his knees, as the attacker, and shot him.
Other security staff joined in shooting Zarhum, the indictment said.
While Zarhum was bleeding and clearly "helpless" on the ground, one of the charged men, David Moyal, slammed him forcefully with a nearby bench, "with the intention of causing him harm, disability or maiming him," the indictment said.
Two other men -- Yaakov Shamba, the soldier, and Eviatar Damari -- then approached Zarhum and forcefully kicked his head and upper body, the indictment states.
After this, Ronen Cohen, the prison guard, threw the bench at the victim to prevent him from moving.
A bystander moved the bench away, but Cohen and Shamba put it back, before Shamba pushed away an onlooker who asked him to stop and kicked Zarhum again, the indictment states.
Wave of violence
The actual gunman in the Beersheva attack, Mohannad Al-Oqbi, was an Arab Bedouin citizen of Israel. He killed an Israeli soldier and wounded 10 more people before police shot him dead.
In the wake of Zarhum's death, which caused shock and triggered soul-searching in Israel, Israeli Prime Minister Benjamin Netanyahu called on citizens not to take justice into their own hands.
People who find themselves "at the site (of an attack) should evacuate the area and let the emergency services do their job," he said, adding that Israel was "a country of law."
"No one will take the law into his own hands. That's the first rule," he said.
Violence has flared in Israel since October
, with Israelis weathering a deadly wave of stabbings, shootings and car-rammings by Palestinians.