Amreeka and Sin Nombre also made the list, which was announced in Los Angeles on Tuesday morning (01Dec09).
The Last Station, which chronicles the final days of Russian author Leo Tolstoy, and the acclaimed Precious scored the most nominations with five each.
Early Oscar favourite The Hurt Locker missed out on a nomination because it was selected last year (08).
Maria Bello (Downloading Nancy), Nisreen Faour (Amreeka), Helen Mirren (The Last Station), Gywneth Paltrow (Two Lovers) and Gabourey Sidibe (Precious) will fight for the Best Female Lead prize, while the Best Male Lead honour will be contested by Jeff Bridges (Crazy Heart), Colin Firth (A Single Man), Joseph Gordon-Levitt, ((500) Days of Summer) Souleymane Sy Savane (Goodbye Solo) and Adam Scott (The Vicious Kind).
Meanwhile, Ethan & Joel Coen (A Serious Man), Lee Daniels (Precious) and Michael Hoffman (The Last Station) lead the Best Director nominations list.
Anvil! The Story of Anvil, Food, Inc., More Than a Game, October Country and Which Way Home will battle for the Best Documentary honours, while A Prophet, An Education, Everlasting Moments, Mother and The Maid will compete for Best Foreign Film.
To be eligible for an Independent Spirit nod, all films must have been made for less than $20 million (£12.5 million). Films must have either screened at a major film festival including Sundance, Toronto or Film Independent’s own Los Angeles Film Festival or had a one-week engagement at a commercial theatre.
The awards will be handed out in Los Angeles on 5 March (10).