The man, Garrett Rolfe, who was fired by the Atlanta Police Department after the June 12 shooting, faces 11 total counts, Fulton County District Attorney Paul Howard said at a news conference.
A second officer, Devin Brosnan, was placed on administrative leave. Brosnan, who is a cooperating witness for the state, faces three charges, including aggravated assault and violation of oath.
Howard said that after the shooting, Rolfe said, "I got him." Brosnan stood on Brooks' body as he was lying on the ground and Rolfe kicked him, according to the district attorney.
He asked both men to surrender by 6 p.m. Thursday.
Brooks, 27, a Black man, was shot in the parking lot of the Wendy's after Rolfe and Brosnan responded to a 911 call that a man who appeared intoxicated was sleeping in his car in the drive-thru.
Brooks, the father of three daughters and a stepson, was shot twice in the back as he ran and died at a hospital following surgery. His death has been ruled a homicide.
In the 911 call, a Wendy's employee told the dispatcher that the customer was parked in the middle of the drive-thru, forcing cars to go around his vehicle. When the dispatcher asked whether the customer had any visible weapons, the employee said: "No, no. I think he's intoxicated."
Rolfe and Brosnan questioned Brooks for more than 25 minutes, body and dash-camera video shows. He told the officers that he had visited his mother's gravesite earlier in the day, gone out drinking with a friend and was dropped off at Wendy's because he was hungry.
During the questioning, Brooks struggled to remember how many drinks he had had and at one point asked the officers whether he could walk home.
"I just don't want to be in violation of anybody," Brooks said, adding, "Let me go. I'm ready to go."
The Georgia Bureau of Investigation, which launched an investigation into the shooting, said Brooks failed a field sobriety test and struggled with the officers as they tried to arrest him.
GBI Director Vic Reynolds said at a news conference Saturday that Brooks was able to get one of the officer's stun guns and that video showed him appearing to run away with the stun gun in his hand.
After running a short distance, Brooks appeared to turn around and point the stun gun at the officer, according to the director. At that point, Rolfe fatally shot Brooks.
Howard, the district attorney, said Wednesday that Brooks "never presented himself as a threat" and appeared "almost jovial." He said Brooks followed every instruction from the officers and was never informed that he was under arrest for driving under the influence.
After he was shot, more than two minutes passed when medical aid was not provided.
"When we examined the videotape and in our discussions with witnesses, what we discovered is during the 2 minutes and 12 seconds, Officer Rolfe actually kicked Mr. Brooks while he laid on the ground, while he was there fighting for his life," Howard said. " Secondly, from the videotape, we were able to see that the other officer, Officer Brosnan, actually stood on Mr. Brooks' shoulders while he was there struggling for his life. "
In addition to felony murder, Rolfe faces charges of aggravated assault with a deadly weapon, criminal damage to property and violation of oath. His attorney said in a statement that the shooting was justified and that Rolfe feared for his life, as well as the lives of the other people in the parking lot, when he fired his weapon.
The death sparked protests in the city and led to Police Chief Erika Shields' resignation less than 24 hours later.
L. Chris Stewart, an attorney for Brooks' family, said his killing was not justified, questioning why the officers did not let Brooks walk home.
"It didn't have to go to that level," Stewart said at a news conference Monday. "And that's what we're saying in America with policing, is this type of empathy is gone. ... Where is the empathy in just letting him walk home?"
Tomika Miller, Brooks' widow, said: "I can never get my husband back. I can never get my best friend. ... It's just going to be a long time before I heal."
Rolfe was reprimanded in a September 2016 use-of-force incident involving a firearm, according to police department records shared with NBC News. No other details were provided.
He also has four citizen complaints on his record, none of which resulted in disciplinary action. Records also show that Rolfe, who was hired in 2013, was involved in five vehicular accidents. One resulted in an oral admonishment and another in a written reprimand, while the rest led to no disciplinary action.
Rolfe's record also shows an additional use-of-firearms incident, in 2015, without note of any disciplinary action.
Comment: In a new development, the Georgia Bureau of Investigation says Atlanta DA jumped the gun with Rayshar Brooks felony murder charges amid reports of police walk-out: