The 68-year-old Scott's death was being investigated as a suicide, Los Angeles County Coroner's Lt. Joe Bale said.
Several people called 911 around 12:35 p.m. to report that someone had jumped from the Vincent Thomas Bridge spanning San Pedro and Terminal Island in Los Angeles Harbor, according to Los Angeles police Lt. Tim Nordquist.
A dive team with Los Angeles Port Police pulled the body from the murky water several hours later, Nordquist said. Scott's body was taken to a dock in Wilmington and turned over to the county coroner's office.
One lane of the eastbound side of the bridge was closed to traffic during the investigation. Cargo vessels moved at reduced speeds through the east side of the port's main channel during the search, said Los Angeles Fire Department spokesman Brian Humphrey.
Investigators found a note in Scott's black Toyota Prius, which was parked on the bridge, according to the Los Angeles Times. That note listed contact information. A suicide note was later found at his office.
The British-born Scott, who lived in Beverly Hills, was producer and director Ridley Scott's brother.
The two brothers ran Scott Free Productions and were working jointly on a film called "Killing Lincoln," based on the best seller by Bill O'Reilly. Their company produced the CBS dramas "NUMB3RS" and "The Good Wife" as well as a 2011 documentary about the Battle of Gettysburg for the History Channel. Ridley Scott's "Prometheus" was a summer blockbuster.
"Top Gun," starring Tom Cruise, was one of the highest-grossing films of 1986. Scott teamed with Cruise again four years later on the hit "Days of Thunder."
Scott frequently worked with Denzel Washington, most recently on the runaway train drama "Unstoppable." The pair collaborated on four other films: "Crimson Tide," "Man on Fire," Deja Vu," and "The Taking of Pelham 123."
In a tweet Sunday, director Ron Howard said, "No more Tony Scott movies. Tragic day."
Other Scott films include "True Romance," written by Quentin Tarantino, "The Fan," with Robert De Niro, and "Enemy of the State," starring Will Smith.
Scott was married to actress Donna Scott, who appeared in several of her husband's films. They have twin sons.
Completed in 1963, the 6,060-foot Vincent Thomas Bridge links rises 185 feet at its highest point above the Los Angeles Harbor. Many have taken their lives by jumping from the span.