Four police officers were assaulted, with one treated for a hand injury, officials said. At least 23 people were arrested.
Video footage showed officers using tear gas to disperse the crowds after police said the protests were considered an unlawful assembly.
"I will protect people's constitutional right to peacefully protest, but violence will not be tolerated. We will protect people's lives, homes, and communities," Missouri Gov. Eric Greitens
wrote on social media.
Protesters made their way to police headquarters and called for police resignations and an economic boycott of St. Louis, the St. Louis Post-Dispatch newspaper reported
'Feels like a burden has been lifted'
Stockley, then a St. Louis officer, fatally shot Smith, 24, after a police chase in December 2011 over a suspected drug deal. After he pleaded not guilty to a murder charge, he waived his right to a jury trial, meaning the ruling was left to the judge.
On Friday, a judge found him not guilty.
"It feels like a burden has been lifted, but the burden of having to kill someone never really lifts," he said in an interview with the St. Louis Post-Dispatch
"The taking of someone's life is the most significant thing one can do, and it's not done lightly. ... My main concern now is for the first responders, the people just trying to go to work and the protesters. I don't want anyone to be hurt in any way over this," he added.
Stockley had said he acted in self-defense and believed Smith was reaching for a gun in his car, but prosecutors accused the officer of planting a silver revolver to justify the shooting.
"I can feel for and I understand what the family is going through, and I know everyone wants someone to blame, but I'm just not the guy," Stockley said.
In his ruling, St. Louis Circuit Judge Timothy Wilson said the state failed to prove that Stockley did not act in self-defense.
St. Louis Circuit Attorney Kimberly Gardner said she was "disappointed" by the decision.
Earlier this week, Smith's fiancée had urged the community to avoid violence.
"However it goes, I ask for peace," Christina Wilson said at a news conference with Greitens.
Authorities had set up barricades around the courthouse and intensified security in preparation for protests, according to CNN affiliate KMOV
"What the country needs to know is, every single person in our country, we have a right to be mad," Al Watkins, an attorney for the fiancee, said after the verdict. "We have a right to disagree. We have a right to express our opinion. We have a right to protest."
"Exploit that right, don't compromise it," he said. "Stay peaceful."
Greitens said the National Guard was activated to protect residents and property after the verdict.
Judge 'agonizingly' reviewed the evidence
Dramatic footage -- captured on the police vehicle dashcam, an internal vehicle camera and cell phone video of the shooting's aftermath -- played a key role in the trial that began August 1.
At the heart of the trial was the question of whether Smith was in possession of a firearm at the time of the shooting. Prosecutors argued that a revolver found in Smith's car had been planted by Stockley to justify the shooting, but the gun was never seen from the multiple cameras that captured Stockley and other officers at the scene.
The prosecution cited footage of Stockley rummaging through a bag in the back of the police vehicle. That was when Stockley retrieved the weapon, they argued. Prosecutors also pointed to the fact that Stockley's DNA had been found on the weapon.
But in his ruling, Wilson said the prosecution's argument was "not supported by the evidence."
"This court ... is simply not firmly convinced of the defendant's guilt," he wrote in his 30-page decision. "Agonizingly, this court has (pored) over the evidence again and again."
The gun was too large, Wilson said, for Stockley to hide it from the cameras at the scene.
Additionally, Wilson found that the prosecution had not sufficiently explained how Smith could have been wounded in his lower left abdomen, given he was sitting inside a car on the driver's side at the time he was killed.
The location of the wound, according to the doctor who conducted the autopsy and testified, could suggest Smith had been reaching to his right for something inside the vehicle, Wilson said.
The judge also cited two witnesses who testified during the trial that the absence of Smith's DNA on the weapon does not necessarily mean he didn't touch the gun.
Wilson said it wouldn't be unusual for Smith to have a gun.
"An urban heroin dealer not in possession of a firearm would be an anomaly," the judge wrote.
A bag with narcotics was found inside Smith's car, according to a responding officer's testimony. It was later revealed to be heroin, the judge said in a footnote to the ruling.
Prosecutors had asked for lesser charges to be considered if Stockley was acquitted of murder. But Wilson declined to consider charges such as involuntary manslaughter because he found the prosecution failed to prove beyond a reasonable doubt that Stockley's "use of force was not justified in self-defense."
Prosecutors argued Stockley intended to kill Smith, citing audio from the internal police vehicle camera during the car chase in which he told his partner, "We're killing this motherf***er."
But the judge noted in his decision that "people say all kinds of things in the heat of the moment or while in stressful situations."
Shooting happened years before Ferguson
Stockley killed Smith years before the fatal shooting of Michael Brown
Initially, state and federal authorities did not prosecute Stockley, but in Ferguson's aftermath, then-St. Louis Circuit Attorney Jennifer Joyce charged him with first-degree murder in May 2016
, citing new evidence.
Stockley left the St. Louis Metropolitan Police Department in August 2013.
Later that year, the St. Louis police board settled a wrongful death suit with Smith's survivors for $900,000
Few police officers ever face trial in shooting deaths, and even fewer are convicted
. Before Friday's verdict, the past year had seen officers acquitted or mistrials declared after jurors deadlocked in several high-profile trials, including at least four since May.
"Officer-involved shootings are very difficult to obtain a guilty verdict," Gardner, St. Louis' chief prosecutor, said Friday.
She later said that in such shootings "we must re-examine not just how we prosecute these cases but how investigate them."
On December 20, 2011, Stockley and his partner, Brian Bianchi, tried to stop Smith after witnessing a suspected drug transaction in a restaurant parking lot, according to a police department report
obtained by the Post-Dispatch
Bianchi told him Smith was reaching for a weapon, the report said. Stockley exited the police SUV carrying his department-issued handgun along with his personal AK-47 pistol. It was against department policy to carry the latter.
Smith tried to speed away, knocking Stockley sideways, and the officer fired several shots at the vehicle, saying he feared for his life and the safety of others, the report said.
Stockley and Bianchi pursued Smith and at some point, the police vehicle crashed into Smith's Buick, the report said.
With Bianchi at the wheel, the officers chased Smith at speeds of more than 80 mph before the crash, according to the criminal complaint.
Smith was alive after the crash when the officers approached his car with their weapons drawn. In the internal report, Stockley said he ordered Smith to show his hands, and believed the suspect was reaching for a handgun between the center console and the passenger seat.
After he fired, striking Smith in the chest, Stockley returned to the police SUV to retrieve materials to render first aid, but when he came back it was too late.
Stockley entered Smith's car "to locate the weapon and render it safe," and removed the ammunition from the silver revolver, he said in the report.
Forensic analysis revealed that Stockley's was the only DNA present on the gun he said belonged to Smith, the criminal complaint said.
Stockley's partner wasn't charged.