A grand jury found "that the use of force by Mr. Raja was unjustified," Palm Beach County State Attorney Dave Aronberg told reporters Wednesday.
Rajas has been arrested, according to Aronberg. He was fired from the police force in November.
Raja was on a burglary detail and in street clothes when he came upon Jones, whose car had broken down on a highway off-ramp early on Sunday morning, October 18.
Jones, 31, was on the phone with an AT&T roadside assistance operator when Raja approached his car, according to the probable cause affidavit.
The recording of the conversation outlined in the affidavit shows that Raja did not identify himself as a police officer before firing his gun six times, hitting Jones three time as he was trying to run away. His body was found in a grassy area 192 feet from his car.
Raja's supervisor testified that he had instructed Raja to identify himself as an officer and to wear a police vest when working on burglary surveillance. According to the affidavit, the vest was found in Raja's unmarked van.
Both men had guns
Jones had legally bought a gun less than 72 hours before he was killed. It was found 41 yards from his body with the safety on and no shots fired, according to investigators.
Raja was heard saying "drop that (expletive) gun right now!" when he called 911 to report that he had shot a person, according to court documents.
Jones was black. Raja is Indian-American. The case marked another in a series of controversial police shootings in the United States that have raised questions about race and policing.
In a statement, Jones family members said they were relieved that Raja was arrested and will face charges.
"While we understand that nothing can bring back our son, brother and friend, this arrest sends a message that this conduct will not be tolerated from members of law enforcement," the family said.