Bob Kendrick, marketing director for the Negro Leagues Baseball Museum, said O'Neil died at a Kansas City hospital.
O'Neil had appeared strong until early August, when he was hospitalized for what was described as "fatigue." He was released a few days later, but readmitted on Sept. 17. Friends said that he had lost his voice along with his strength. No cause of death was immediately given.
Always projecting warmth, wit and a sunny optimism that sometimes seemed surprising for a man who lived in a climate of racial injustice for so long, O'Neil remained remarkably vigorous well into his 90s. He became as big a star as the Negro League greats whose stories he traveled the country to tell.
He would be in New York taping the "Late Show With David Letterman" one day, then back home on the golf course the next day shooting his age, a feat he first accomplished at 75.
"But it's not a good score any more," he quipped on his 90th birthday.
O'Neil had long been popular in Kansas City, but he rocketed into national stardom in 1994 when filmmaker Ken Burns featured him in his groundbreaking Public Broadcasting Service documentary "Baseball."
The rest of the country then came to appreciate the charming Negro Leagues historian as only baseball insiders had before. He may have been, as he joked, "an overnight sensation at 82," but his popularity continued to grow for the rest of his life.
Few men in any sport have witnessed the grand panoramic sweep of history that O'Neil saw and felt and experienced in baseball. A good-hitting, slick-fielding first baseman, he barnstormed with Paige in his youth, twice won a Negro Leagues batting title, then became a pennant-winning manager of the Kansas City Monarchs.
As a scout for the Chicago Cubs, he discovered and signed Hall of Famers Lou Brock and Ernie Banks.
In 1962, a tumultuous time of change in America when civil rights workers were risking their lives on the back roads of the Deep South, O'Neil broke a meaningful racial barrier when the Chicago Cubs made him the first black coach in the major leagues.
Jackie Robinson was the first black with an opportunity to make plays in the big leagues. But as bench coach, O'Neil was the first to make decisions.
He saw Babe Ruth hit home runs and Roger Clemens throw strikes. He talked hitting with Lou Gehrig and Ichiro Suzuki.
"I can't remember a time when I did not want to make my living in baseball, or a time when that wasn't what I did get to do," he said in an interview with The Associated Press in 2003. "God was very good to old Buck."
Born in 1911 in Florida, John "Buck" O'Neil began a lifetime in baseball hanging around the spring training complex of the great New York Yankee teams of the '20s. Some of the players befriended the youngster and allowed him inside.