The Los Angeles County Coroner's office said Scott's death was being investigated as a suicide.
British-born Scott, brother of Alien director Ridley, shot to fame in the 1980s with a string of action films.
The 68-year-old's blockbuster hits included Crimson Tide, Days of Thunder and Beverly Hills Cop II.
The coroner said Scott jumped from the Vincent Thomas Bridge, which spans San Pedro and Terminal Island in Los Angeles.
Lt Joe Bale, from the coroner's office, said the director was seen parking his car and jumping into the water at about 12:30 (19:30 GMT) on Sunday.
His body was recovered from the harbour less than three hours later.
"We will go where the facts take us. We have no reason to believe it was not a suicide," Lt Bale told the BBC.
Fellow director Ron Howard said on twitter "No more Tony Scott movies. Tragic day."
Duncan Jones, director of Source Code and Moon, said "Just heard about Tony Scott news. Horrible Tony was a truly lovely man who took me under his wing & ignited my passion to make films."
Scott, born in Northumberland, was famous for his fast-paced blockbusters, and carved out a distinctive style to his films using fast editing and digital effects.
He made a number of films with actor Denzel Washington, including Man on Fire and most recently Unstoppable. More recently, he had been producing for television as well as films.