Sgt. Dominic Vaca, 43, was airlifted to the hospital but succumbed to his injuries Monday, Sheriff John McMahon said in a video message posted on Twitter.
"The gunshot wound he sustained earlier today was too severe for him to overcome. Our prayers are with him and his family as we all mourn this difficult time," the sheriff said.
Law enforcement agencies held the procession for Vaca, a 17-year veteran of the department, outside the hospital where he passed away.
Vaca was a sergeant at the Morongo Basin Station.
Shortly after 12:30 p.m. Monday, deputies attempted to conduct a traffic stop after spotting the motorcycle without a license plate near the intersection of Paxton Road and Imperial Drive. The man on the motorcycle refused to pull over and a chase ensued, the Sheriff's Department said in a statement.
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During the pursuit, the suspect "bailed out of the vehicle" near Dumosa Avenue and Sunnyslope Drive and ran into the desert, the news release said.
"A short time later, they located the motorcycle and the rider was gone," Sheriff McMahon said.
As deputies approached the motorcycle and attempted to find the rider, he started firing at responding deputies, striking Vaca.
"A short time later, the suspect was located and he started shooting at the additional deputies. They returned fire and the suspect is deceased," the sheriff said, adding that a handgun was found at the scene.
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The desert area where Vaca was shot is north of Highway 62 and west of Joshua Tree and Twentynine Palms.