After three weeks of testimony, the jury of eight women and four men took eight hours to reach their decision. There were tears on both sides when the verdict was read just before 4 p.m. Monday.
Thomas, 37, died five days after a violent confrontation with six officers in July 2011. The incident was caught on surveillance video.
Former Fullerton police officer Manuel Ramos was charged with second-degree murder and involuntary manslaughter, and former police corporal Jay Cicinelli was charged with involuntary manslaughter and excessive force. Both men pleaded not guilty to the charges.
When the "not guilty" verdict was read, Cicinelli's attorney slammed his fist on the table and hugged his client, and Cicinelli started crying.
Prosecutors argued that surveillance video shows proof that Ramos abused his authority, turning a routine encounter into a deadly one with his threat. But defense attorneys said the video showed that officers followed their training and police department policy when dealing with an uncooperative, combative suspect.
The two sides also differed on what the cause of death was in Thomas' death. The defense claimed Thomas died because of an enlarged heart caused by years of methamphetamine use, but prosecutors said he died from a lack of oxygen caused by chest compression and facial injuries.
Ramos was the first law enforcement officer in Orange County to be charged with a homicide for an on-duty death.
The FBI opened an investigation shortly after Thomas's death to determine if his civil rights were violated. Now that the state trial has ended, the FBI says it will continue with that investigator.
Following the verdict, Thomas' parents spoke to the media and expressed their shock and outrage.
"I'm just horrified. They got away with murdering my son," said Kelly Thomas' mother, Cathy Thomas. "I guess it's legal to go out and kill now. He was so innocent. It just isn't fair at all."
His father, Ron Thomas, said the "defense lied continuously" during the trial and justice wasn't served.
"What this means is all of us need to be very afraid now. It's carte blanche, for police officers everywhere can beat us, kill us, whatever they want. Because it has been proven right here, today, they'll get away with it," said Ron Thomas.
Defense attorney John Barnett maintained that the officers did nothing wrong.
"These peace officers were doing their jobs. They were operating as they were trained and they had no malice in their hearts. They were not out to get somebody that night. They were working...They committed no crime," Barnett said after the verdict.
Ron Thomas said a civil suit will likely continue and he hopes the federal government will get involved.
Kelly Thomas' parents joined supporters at a memorial in Fullerton Monday night, demanding justice.
"I just can't believe it. I'm in shock. I feel like the justice system failed us," said Mari Bermudez of Orange.
Meantime, after the acquittals of Cicinelli and Ramos, Orange County's district attorney said his office will drop charges against a third officer involved in the struggle that led to Kelly Thomas' death. Former Fullerton officer Joseph Wolfe would no longer face charges of involuntary manslaughter and excessive force.