Police told U-T San Diego that they received a report at 9:12 a.m. Saturday that a man pointed a gun at the head of another man at an apartment complex.
Witnesses said they saw the man driving away in a silver Volkswagen sedan.
Officers spotted the car on Sea World Drive, pulled over the driver and told him to get out and put his hands in the air.
"The suspect did not comply. Instead, he exited the vehicle, went over to the passenger side ... and pulled out what appeared to be some sort of object, and raised it toward the officers. At this point, one officer fired his weapon," Police Lt. Jorge Duran said.
The man was taken to the hospital, where he died.
U-T San Diego said it remains unclear what the man grabbed, but Duran said a knife was found on the ground near the vehicle.
Witnesses said that the man, whose name is not being released, made an aggressive gesture with both of his hands extended before being hit.