Lee, 55, was going to be in Venice in conjunction with "Bad 25", that will explore the making and impacts of Jackson's album which was released 25 years ago.
The film will screen in the official selection but out of competition, said The Hollywood Reporter.
The award and the screening of the documentary will represent Lee's 9th trip to the Venice Lido in an official capacity.
The Glory to the Filmmaker award is presented to a personality that brought "great innovation to contemporary cinema".
"Spike Lee is a bold and creative spirit, the author of daring and corrosive films, often unpredictable and provocative in the best sense of the word. He creates films that challenge us to rethink our prejudices and our preconceptions," Venice artistic director Alberto Barbera said in a statement.
The award will be presented to Lee on August 31, ahead of the screening of "Bad 25". The 69-year-old festival runs August 29-September 8.
Lee is a regular on the Venice Lido, with eight previous films screening during the festival. Additionally, Lee was a member of Venice's International Jury in 2004.
Previously, the Glory to the Filmmaker award has been presented to Al Pacino last year, Mani Ratnam in 2010, Sylvester Stallone in 2009, Agnes Varda in 2008, and Abbas Kiaristami in 2008.
