The hilarious though dark-tinged tale of a deeply dysfunctional family also won the supporting-actor award for Alan Arkin; best director for the husband-and-wife team of Jonathan Dayton and Valerie Faris, and best first screenplay for Michael Arndt.
Arkin won for his role as an obscenity-spewing, heroin-snorting grandfather training his granddaughter (Abigail Breslin) for a saucy dance performance at a children's beauty pageant.
He thanked his co-stars, calling them "the most cohesive, loving" group of actors he had worked with.
Arkin's competition for supporting actor at the Spirit Awards included "Little Miss Sunshine" co-star Paul Dano, who played his grandson, a morose youth maintaining a vow of silence.
Arndt thanked organizers for having a category for first-time writers.
"Anybody who sits down to write a screenplay without any prior credits, I think it's an act of insanity," Arndt said.
The awards honoring the best in independent film were the latest in a string of honors for "Little Miss Sunshine" since its premiere at last year's Sundance Film Festival.
Its Oscar nominations included best picture and supporting-acting slots for Arkin and Breslin.
"I can only hope that filmmakers out there trying to get their first film made or their second or third film and are having some trouble can find some hope from what has happened to us on this movie," Dayton said. "We were dead ... in the studio system. They had given up on us and thankfully people in the independent world stuck with us."
The lead-acting Spirit Awards went to the stars of another Oscar contender, the classroom drama "Half Nelson." Ryan Gosling played an inspiring teacher battling a severe drug habit and Shareeka Epps won for her role as a bright student who becomes both his protege and counselor.
Gosling had a best-actor Oscar nomination for "Half Nelson," which also debuted at Sundance last year.
A third Sundance premiere, "Friends With Money," took the supporting-actress Spirit Award for Frances McDormand as a fashion designer who finds that wealth does not necessarily buy happiness.
The top prize winner at Sundance last year, the teen drama "Quinceanera," won the John Cassavetes Award for a film shot for less than $500,000.
"Quinceanera" centers on a Mexican-American teen ostracized by her family after she becomes pregnant.
Jason Reitman won the screenplay award for the tobacco-industry satire "Thank You For Smoking," which he also directed.
Robert Altman — nominated as best director for his final film, "A Prairie Home Companion" — was saluted with an honorary Spirit Award for his lifetime devotion to independent film. Altman died last November.
Spirit Awards organizers have created a new prize, the Robert Altman Award, which beginning next year will be given out to a film's director and acting ensemble — a nod to Altman's gift for overseeing large, overlapping casts.
Other Spirit Award winners were:
- Best foreign film, "The Lives of Others," Germany, directed by Florian Henckel von Donnersmarck.
- Best documentary, "The Road to Guantanamo," directed by Michael Winterbottom and Mat Whitecross.
- Best first feature, "Sweet Land," directed by Ali Selim.
- Best cinematography, Guillermo Navarro, "Pan's Labyrinth."
The Spirit Awards are presented by the cinema group Film Independent to films costing less than $20 million to produce. Other guidelines for nominations include a film's uniqueness of vision, original, provocative subject matter and percentage of financing that comes from independent sources outside the Hollywood studio system.
By David Germain