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The new Chief George Gascon, 55, is being sworn in this afternoon.
Fong, who announced her retirement in December after nearly five years as chief, declined to hold a news conference or issue a public statement.
About 200 officers and staff attended a farewell party for Fong on Thursday afternoon at the Hall of Justice, according to police spokeswoman Sgt. Lyn Tomioka.
Fong, 53, is spending the remainder of her last day catching up on paperwork, Tomioka said.
She was liked and admired by many in the department for her dedication and fairness to her officers, Tomioka said.
Fong's leadership style rankled some in the department, who accused her of not standing up publicly enough to defend officers against criticism. Others complained about how she handled the disciplining of officers accused of misconduct.
"She didn't go out looking for allegations of misconduct, but when they were presented to her, she had to investigate them," Tomioka said.
Fong withstood a lot of interdepartmental criticism, Tomioka said, but never changed her personality.
"She is by the book, she didn't waver, it was the same for everybody," Tomioka said.
Fong, who was named chief by Mayor Gavin Newsom in 2004 and became the city's first female police chief, inherited a department that had been troubled by scandal, including allegations of misconduct by command staff during the so-called Fajitagate scandal.
During her tenure she oversaw departmental reforms such as the implementation of foot patrols, new zone policing strategies credited with recent drops in violence, and efforts to foster better relationships between police and the community.
Fong was widely praised by city leaders for her integrity, honesty and strong work ethic.
A San Francisco native, Fong began her career with the San Francisco Police Department as an officer in 1977. She ends it just one week shy of her 32nd anniversary with the department.
Fong has not discussed what she intends to do next, but Tomioka said she'll likely take some time off, having never taken a vacation during her five-year tenure as chief.
Gascon, the former police chief of Mesa, Ariz.., has pledged to continue reforming the department.
"We're sad to see Chief Fong go, but we're certainly looking forward to him coming in," Tomioka said.
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