Nelson, who had pancreatic cancer, died at his home in the Washington suburb of Bethesda, Maryland, said Richard Cooper a family friend and longtime Times associate.
Nelson spent more than 35 years with the Los Angeles Times, stepping down as its chief Washington correspondent in 2001. He joined the Times in 1965 and in 1970 began working in its Washington bureau. He was bureau chief from 1975 to the end of 1995.
As a reporter with The Atlanta Constitution in 1960, he won the Pulitzer Prize for local reporting for exposing malpractice and other problems at the 12,000-patient state mental hospital in Milledgeville, Georgia.
"Jack was a reporter's reporter," said Doyle McManus, Washington columnist for the Los Angeles Times. "He maintained that the main thing people want from newspapers is facts - facts they didn't know before, and preferably facts that somebody didn't want them to know. Jack was tolerant of opinion writers; he respected analysis writers, and he even admired one or two feature writers. But he believed the only good reason to be a reporter was to reveal hidden facts and bring them to light."
Nelson began focusing on civil rights issues when he opened the Los Angeles Times bureau in Atlanta in 1965.
"He carried his investigative abilities forward and applied them to what was going on in the South during the civil rights era," said veteran journalist Gene Roberts, an author of the book "The Race Beat: The Press, the Civil Rights Struggle and the Awakening of a Nation." "Jack had what the military calls 'command presence.' He was very self-confident and his earnestness and authority communicated itself."
Two of Nelson's five books stemmed from his civil rights reporting: "The Orangeburg Massacre" (1970), co-authored with Jack Bass, which chronicled the 1968 incident in which police fired into a crowd of young protesters at South Carolina State College, killing three, and "Terror in the Night: The Klan's Campaign Against the Jews" (1993).
"A reporter likes to pride himself on being as objective as he can and, you know, tell them both sides of the story. Well, there's hardly two sides to a story of a man being denied the basic right to vote," Nelson said in an interview in 2004. "There's no two sides to a story of a lynching. A lynching is a lynching."
Nelson covered presidential administrations from Richard Nixon to Bill Clinton. During the Watergate scandal, he scored an exclusive interview with a security guard for the Nixon re-election campaign who had been involved in the break-in at the headquarters of the Democratic National Committee.
John Howard Nelson was born on Oct. 11, 1929, in Talladega, Alabama, and graduated from high school in Biloxi, Mississippi. He was a reporter for the Biloxi Daily Herald from 1947 to 1951 before serving a stint in the U.S. Army. He joined The Atlanta Constitution in 1952.
Survivors include his wife, journalist Barbara Matusow, and three children, Karen, John and Steven, from his marriage to Virginia Dickinson.