It was passed over in the acting categories, despite Ali and Harris being considered strong contenders for Oscar nods.
Starring Mahershala Ali and Naomie Harris, Barry Jenkins's "Moonlight" tells the life story of a young African-American man struggling to find his place as he grows up in a rough neighborhood of Miami.
It was nominated in six categories, including best feature, best director and best screenplay.
It was passed over in the acting categories, despite Ali and Harris being considered strong contenders for Oscar nods. The entire cast, Jenkins and casting director Yesi Ramirez will get the special Robert Altman Award.
"American Honey," written and directed by British filmmaker Andrea Arnold and starring Sasha Lane and Shia LaBoeuf, also secured six nominations, including female lead, supporting female and male.
Kenneth Lonergan's New England-based family drama "Manchester by the Sea," which has given Casey Affleck an early lead in the race for the best-actor Oscar, got five nominations.
The movie, which opened on Friday to some of the best reviews of the year, is up for best feature and best actor and supporting actor.
"Jackie," Pablo Larrain's political drama focusing on former US president John F Kennedy's assassination through the eyes of First Lady Jacqueline Bouvier Kennedy, picked up nominations for directing, editing and feature, as well as nod for Natalie Portman's acclaimed performance in the title role.
The Film Independent Spirit Awards are seen as an strong indicator of independent movies that could win Oscar glory.
"Now more than ever, the voices of independent artists play a critically important role in our culture," said Film Independent's president Josh Welsh.
"The films we celebrate at this year's Spirit Awards embody the diversity, innovation and uniqueness of vision that we champion all year long."
The winners will be announced on February 25, a day before the Academy Awards.