The win is the latest honor for the coming-of-age drama about a young, gay black man in a rough Miami neighborhood.
The film's director, Barry Jenkins, also won as did supporting actor Mahershala Ali and cinematographer James Laxton.
Isabelle Huppert won best actress for two films -- "Elle" and "Things To Come" -- while Adam Driver took home the best actor award for "Paterson."
The "Moonlight" win comes days after the film made history at the 26th Annual Gotham Independent Film Awards by winning four prizes and becoming the first movie to win both best feature and the audience award in the same year.
The film also has been nominated for 10 Critics' Choice Awards.
The winners from the films selected by the L.A. Film Critics Association will be honored at an event in January.
Runner-up: "La La Land"
Barry Jenkins, "Moonlight"
Runner-up: Damien Chazelle, "La La Land"
Adam Driver, "Paterson"
Runner-up: Casey Affleck, "Manchester by the Sea"
Isabelle Huppert, "Elle" and "Things to Come"
Runner-up: Rebecca Hall, "Christine"
Best supporting actor
Mahershala Ali, "Moonlight"
Runner-up: Issey Ogata, "Silence"
Best supporting actress
Lily Gladstone, "Certain Women"
Runner-up: Michelle Williams, "Manchester by the Sea"
Best animated film
Runner-up: "The Red Turtle"
Best foreign-language film
Runner-up: "Toni Erdmann"
"I Am Not Your Negro"
Runner-up: O.J.: "Made in America"
Efthymis Filippou and Yorgos Lanthimos, "The Lobster"
Runner-up: Kenneth Lonergan, "Manchester by the Sea"
Bret Granato, Maya Mumma, Ben Sozanski, "O.J.: Made in America"
Runner-up: Tom Cross, "La La Land"
Best production design
Ryu Seong-hee, "The Handmaiden"
Runner-up: David Wasco, "La La Land"
Best music score
Justin Hurwitz, Benj Pasek, Justin Paul, "La La Land"
Runner-up: Micah Levi, "Jackie"
James Laxton, "Moonlight"
Runner-up: Linus Sandgren, "La La Land"
Lifetime achievement award