The decision to charge Deputy Ivory J. Webb, 45, was announced by San Bernardino County District Attorney Michael A. Ramos.
Sheriff Gary Penrod said Webb will remain on paid administrative leave during the investigation into the shooting of Air Force Senior Airman Elio Carrion, 21.
"I respect the decision of the district attorney's office," Penrod said.
It is the first time the county's prosecutors have filed charges against a lawman for an on-duty shooting.
Webb's arraignment was set for Wednesday. If convicted, he could face up to 18½ years in prison.
The charge includes the special allegations of infliction of great bodily injury and use of a firearm, Ramos said at a news conference. In California, such enhancements can result in extra prison time.
Carrion, an Air Force security officer just back from Iraq, was a passenger in a Corvette that police chased at high speed on the night of Jan. 29 until the Corvette crashed into a wall in Chino, about 45 miles east of Los Angeles.
A grainy videotape shot by a bystander showed Carrion on the ground next to the car with Webb standing and pointing at gun at him.
A voice appears to order Carrion to rise, but when the airman appears to begin complying, the deputy shoots him three times. Carrion was shot in the chest, shoulder and thigh and was hospitalized for several days.
Authorities found no weapons on Carrion or the driver, Luis Escobedo.
Prosecutors announced they were charging Escobedo with a felony of attempting to evade a peace officer while driving recklessly and misdemeanor driving under the influence. He was expected to surrender Wednesday. The maximum penalty if convicted would be 3½ years in prison.
The FBI is investigating possible civil rights violations. The sheriff's department conducted its own probe and gave the results to the district attorney's office.
At the time, the sheriff said the videotape "arouses a lot of suspicion," but he pointed out that it is fuzzy and contains gaps.
"In any type of investigation, it is the responsibility of the Sheriff's Department to put together all the facts," Penrod said Tuesday. "The district attorney's role is to take those facts and determine whether there is sufficient evidence to issue a criminal complaint. Obviously that was their choice in this investigation."
Ramos assigned two top attorneys to review the shooting and requested an FBI enhancement of the videotape.
Last month, Carrion's wife insisted he did nothing wrong and demanded that the police officer be arrested.
"I can't sleep at night no more … knowing that we could have lost him. There's just no words for it," Mariela Carrion told CBS News correspondent Sandra Hughes.
She's still a teenager and has been married to Elio for two years.
Mariela finds it hard to understand why her husband, who survived six months as a senior airman in Iraq, was.
"I went to the crime scene, and I saw the car and I saw his clothes there. And at that point, I just felt, 'Oh, my god. What happened?"
If a passerby hadn't happened to take the video, asserts Mariela, "They would have let my husband bleed to death, and they would have switched that whole story around.
"I just want that man to be placed in jail," she insists. "I want justice. And I'm not giving up."