It happened on Mowry Avenue and Blacow Road. Police were there for hours and cleared the scene.
"He was crying on the ground and he was bleeding on the ground and I'm like, 'Oh my God,'" said Gemina Marin-Robinson who took cellphone video of the incident. "I saw the officer telling him to stop, telling him to drop what he had in his hand. And then he proceeded to run, chasing him -- the young man."
She said she was shocked at what happened next. "I thought he was pulling his taser out but he pulled out his gun," Marin-Robinson told ABC7 News. "I said, 'Oh my God he just shot him.' Shot him three times."
Fremont police say just before 4 p.m. someone flagged down an officer to report the man.
"A citizen basically contacted him, advising him that a subject was waving a pipe -- threatening people," said Sgt. Ricardo Cortes of the Fremont police.
The officer found the man in the shopping center. "There was some sort of foot pursuit," Cortes added. "Confrontation which led to shots being fired."
Police say they're still investigating exactly what happened during that confrontation, but they did recover the pipe.
They say the man was taken to a trauma center and his condition is not known. The officer has been placed on administrative leave. This is the fourth officer-involved shooting in Fremont this year.