After an initial investigation, authorities said the blast had been self-inflicted.
The grand jury was looking at whether it was an accident, suicide or even a possible slaying.
It concluded there was no forensic evidence, including DNA, that indicated the deputy who pulled Johnson over had fired the gun.
"The grand jury finds ... that Deputy Joe Sullivan was in his patrol car at the time of Billey Joe Johnson Jr.'s death," the ruling said.
The ruling said Johnson's hands tested positive for gunpowder residue and there were no other injuries on his body. The grand jury said there were no other people involved in the shooting.
The mystery surrounding the athlete's death has inflamed suspicion, with Johnson's family and the local chapter of the National Association for the Advancement of Colored People rejecting the notion of suicide. They said he had too much to live for including a chance of playing in college and maybe the NFL.
"I ain't buying that," his mother, Annette Johnson said of the grand jury's conclusion. "We are going further and we are going higher."
Dozens of people - mostly family members and friends - prayed outside the George County Courthouse in Lucedale in southern Mississippi before going inside to hear the report read aloud.
Johnson family attorney Jerome Carter has said his independent investigation of the case will continue.
The NAACP said it would submit its evidence to the U.S. Justice Department and ask for a federal probe.
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