The man was then taken to San Francisco General Hospital, where he underwent surgery. Suhr had described him as being in "very, very critical condition."
A hospital spokesman said he died shortly after 1 p.m. His identity has not yet been released.
John Visor and Stephanie Grant, who live in a tent on Shotwell Street, said they saw the shooting, KQED's Alex Emslie reports. Visor identified the man as "Jose" and said he had known him for about a year.
“He didn’t charge at no officers," Visor said. "He was going in circles because he wasn’t understanding what they were saying.”
Grant said the man was always friendly and she'd never seen him threaten anyone with a knife that he carried for protection while collecting bottles and cans.
"He doesn’t understand English," she said, adding the incident played out in less than a few minutes. "It shouldn’t have happened that way at all."
Visor said his friend's knife was stuck, blade down, in the man's belt.
"The knife was up on his hip the whole time," Visor said. "When the last shot hit him, that's when he fell, and that's when the knife fell out and hit the ground."
Suhr said officers reported after the shooting that they had fired beanbag rounds.
"I'll give you the quote," he told reporters as he read from a computer-assisted dispatch report. "It says 'extended range impact weapon, several times. Subject did not go down, got up and charged with the knife.' "
Visor spoke through tears about the man he said he'd shared a nearby room with before he lost the apartment.
"He was a good friend," Visor said. "He never hurt nobody. Only thing he did was pick up cans and bottles for a living."