The film, which is directed by and stars Favreau, is about a chef who operates a food truck after his restaurant is closed.
The film comes with a $25,000 prize, which Favreau said he would donate to City Harvest, a food rescue organization in New York City.
Winning the audience award for best documentary was Alan Hicks' Keep on Keepin' On, about the relationship between jazz legend Clark Terry and blind piano prodigy Justin Kauflin.
"These films happen to share the common theme of following one's dreams, the challenging journey to achieve them, and how it cannot be done without true friendship, family and support,” Genna Terranova, the festival’s director of programming, said.
Chef debuts in theaters May 9.