Body-camera video from another officer showed the ex-cop, Dominique Heaggan-Brown, fired the second bullet into Smith's chest after the suspect hurled his weapon over a fence and had his hands near his head, according to the complaint.
Smith had been armed with a Glock .40-caliber model 22 semi-auto handgun with an extended magazine but Heaggan-Brown's body camera showed he threw the weapon into an adjacent yard as he was shot the first time, the complaint said.
"A review of both Heaggan-Brown's body camera and (the other officer's) camera confirm that Smith was unarmed at the time of the second shot," said the complaint filed by the Milwaukee District Attorney's office.
It's unclear whether Heaggan-Brown has an attorney. His bail was set Friday at $100,000, CNN affiliate WITI reported.
Smith's family, in a statement, called the criminal charges "the first step in holding (the) officer accountable," according to WITI.
The statement added: "We always believed that Sylville should be alive today, and that this rogue officer was completely wrong. Though the decision to prosecute cannot bring back Sylville, justice is needed for our family as we continue to move through deep grief and seek justice for his wrongful death."
At a news conference, police Chief Edward Flynn said the 1.69 seconds the complaint stated separated the two shots was of concern to officers making life-and-death decisions on the street.
"Quite honestly ... the fact that two shots fired were in 1.69 seconds and one is legal and one's not -- that's a little bit difficult to understand or explain to the rank and file," he said.
"They understand that the defendant did some pretty bad things ... but I think in terms of their operating assumption, the fact is, if you're in a combat situation facing an armed defender, 1.69 seconds is less than two full heartbeats."
Racially charged shooting followed traffic stop
Milwaukee, long torn by racial tensions, exploded with protests last summer after Smith, who is black, was killed while running from a traffic stop. Heaggan-Brown also is African-American.
For two nights, protesters torched a half dozen businesses, smashed cars and hurled rocks at police.
Body-camera footage shows Smith running from a Ford Fusion and heading into a yard with a weapon in his hand, the complaint said.
Smith slipped near a chain-link fence between two houses, according to the complaint. He rose back up, the gun still in his right hand, and turned toward the approaching officers.
Facing the cops, Smith raised the gun up and threw it over the fence, the complaint said. His weapon was not discharged.
Heaggan-Brown fired the first shot when Smith raised the weapon, sending the suspect to the ground on his back, the court document said. The bullet passed through his right bicep and lodged in a window casement.
The other officer's body camera also captured Smith falling on his back, the complaint said.
'Smith ... had his hands near his head'
"Heaggan-Brown is observed standing a short distance from Smith with his weapon pointed down at Smith when Heaggan-Brown discharges a second shot from his weapon at what appears to be Smith's chest," the complaint said.
Smith's arms and legs continued to move. The complaint said he "appears to bring his left hand toward his waistband."
"A review of the body camera video from both (officers) confirms that at the time of the second shot, Smith was unarmed and had his hands near his head," according to the court document.
In the body camera audio, which was activated about 30 seconds after the shooting, Heaggan-Brown is heard yelling at Smith: "Stop reaching!" The ex-cop moved Smith's hand away from his waist, the complaint said.
The complaint said Heaggan-Brown told investigators Smith stopped at the fence and raised his weapon. The former officer said he fired once, causing the weapon to "fly out of Smith's hand and over the fence."
Heaggan-Brown said he believed Smith "was reaching for his waist so he discharged his weapon a second time."
Body camera footage showed that none of the officers searched Smith for a second firearm after the shooting.
"In fact, when Smith demonstrably reaches for his waistband after being shot the second time, Heaggan-Brown does not discharge his weapon, but moves Smith's hand away with his own hand," the complaint said.
An autopsy revealed that Smith suffered a gunshot wound through his right upper arm and another to the right upper chest.
Officer loses job amid sex assault allegations
Police have said the former officer shot Smith after he failed to comply with orders to put down his gun, which was loaded with 23 rounds.
Smith -- described by family as a caring father, a loyal friend and popular dancer in Milwaukee's thriving hip-hop scene -- was known to Heaggan-Brown before the fatal encounter in August, Smith's relatives and friends said at the time.
The officer was fired in October amid allegations of sexual assault that came to light after the fatal shooting.
Heaggan-Brown watched TV coverage of the violent street protests that followed the Smith shooting at a bar with a man who later accused the officer of sexual assault, according to a separate complaint.
The unidentified man told investigators that Heaggan-Brown sexually assaulted him while off-duty two days after the Smith shooting on August 13.
Heaggan-Brown rose from a police apprenticeship program to become a cop on the rough-and-tumble streets of the city's northwest side.
After the shooting, the officer's name and photo were widely circulated on social media, with angry comments from people threatening to have him killed.
Some online posters described encounters with what they said was an overzealous officer.
Heaggan-Brown had six years of service with the Milwaukee police, three as an officer, officials said. He entered the department as part of an apprentice program that recruits high school students and requires they complete college credits.