One of the men, Oliver Barcenas, ran from officers and tossed a loaded Glock pistol before an officer shot him, striking him two times in the back.
"I know when you see a video and we have limited facts right now, it's very difficult because people want answers and that is the purpose of all these investigations," said San Francisco Police Chief William Scott.
VIDEO: Bodycam video shows SFPD officer shooting man in back
VIDEO: Bodycam and surveillance video show officer-involved shooting in SF
Members of the community were concerned about how quickly the incident escalated on a street known for its nightlife and questioned the independence of the internal investigation.
"I hope that the independent investigations in this matter are truly independent. That the level of this transparency continues," said San Francisco Supervisor Aaron Peskin.
Police have yet to release the name of the officer involved in the shooting. No officers or bystanders were hurt.