Chief Michael Pimentel stopped Joshua Manuel Lopez, 24, around 11:30 a.m., at which time the two got into a confrontation, the Bexar, Texas, County Sheriff's Office said.
Pimentel sustained gunshot wounds to the stomach and shoulder.
"You know, on even a quiet, peaceful day in South Texas in a small town, it can turn deadly in an instance and it re-enforces the dangers our law enforcement officers face every single day," Bexar County Sheriff Susan Pamerleau told KSAT-TV, San Antonio.
The chief was airlifted to University Hospital, where he died of his injuries.
"We have taken responsibility for this continued investigation. It's a very small agency, the chief and a few other officers, and we have the investigative capabilities to investigate this," said Pamerleau.
Lopez was charged with capital murder and has an existing warrant for graffiti.
The San Antonio Police Department offered its condolences on Twitter.
Our thoughts are with the Elmendorf P.D. And with the family of Elmendorf Police Chief Michael Pimentel, who was... http://t.co/LgR6bOnw88— SA Police Dept (@SATXPolice) August 23, 2014