Lee will collect the honour at the Film Society Awards Night on May 3, when attendees will see a reel of Lee's film-making highlights followed by an on-stage interview.
Festival organisers have also scheduled a screening on May 2 of Lee's documentary When the Levees Broke; A Requiem In Four Parts (Acts II & III), which takes stock of the devastation caused in Louisiana in 2006 by Hurricane Katrina. A full four-hour screening will run on May 4.
Lee is well known to the SFIFF community. The festival screened his early short Joe's Bed-Stuy Barbershop: We Cut Heads in 1983, and three years later hosted the world premiere of She's Gotta Have It, when Lee regaled the audience in an on-stage interview by flashlight after a power cut interrupted the screening.
'No American director of the last 25 years has done more to lever open and examine the inner workings of American society than he has,' San Francisco Film Society executive director Graham Leggat said.
'Spike's many and wide-ranging films, and the many more that he is still to make, constitute an irreplaceable and invaluable touchstone in contemporary world cinema.'
Previous Film Society Directing Award recipients include Robert Altman, Akira Kurosawa, Abbas Kiarostami, Werner Herzog, Milos Forman, Warren Beatty and Clint Eastwood.
As previously announced, Peter Morgan will collect the Kanbar Award for excellence in screenwriting, and George Lucas will collect the one-time-only Irving M Levin Award honouring a man who embodies the spirit and entrepreneurship of festival founder Levin.