D'Onofrio was born in Bensonhurst, Brooklyn. He is of Italian descent, with ancestors from Sicily. His parents, Gennaro and Phyllis D'Onofrio, an interior designer/theater-production assistant, and server, respectively, met while Gennaro was stationed in Hawaii with the U.S. Air Force. In 1956, they had their first child, Antoinette. Their second child, Elizabeth (born 1957), is an actress and drama coach residing in Fort Myers Beach, Florida, and then Vincent was born, the youngest of the three siblings. He was raised in Hawaii and Colorado during his early years.
D'Onofrio's parents divorced when he was young; his mother later married George Meyer. He became step-brother to Meyer's children from a previous marriage (Guy and Connie). The family moved to the Hialeah, Florida area. D'Onofrio described himself as a shy boy who spent "a lot of time in my room, staying in my head", later became interested in magic and sleight of hand, tricks he learned from Cuban entertainers who owned a small magic shop.
In his teens, he worked backstage in set building and sound production at a number of run by his father. He graduated from Hialeah-Miami Lakes Senior High School.