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.
In February 2006, it was widely thought that a special 12-person committee commissioned to render final judgments on Negro Leagues and pre-Negro league figures would make him a shoo-in for the Baseball Hall of Fame. It would be, his many fans all thought, a fitting tribute to the entire body of his life's work.
But when word came from Florida that day that 16 men and one woman had been voted in, he was not among them. For reasons never fully explained, he fell one vote short of the required three-fourths.
Several hundred of his friends and admirers had gathered at the Negro Leagues Museum for what they thought would be a celebration. Instead, they stood in awkward, restless silence as the old man once again -- (for how many times in his long, eventful life?) brushed bitterness aside.
"Shed no tears for Buck," he told them. "I couldn't attend Sarasota High School. That hurt. I couldn't attend the University of Florida. That hurt.
"But not going into the Hall of Fame, that ain't going to hurt me that much, no. Before, I wouldn't even have a chance. But this time I had that chance.
"Just keep loving old Buck."
But among his close friends, few believed that his heart wasn't really broken.
"It is clear the Baseball Hall of Fame has made a terrible error in not inducting Buck on this ballot," Missouri Rep. Emanuel Cleaver said. "It is rare that an entire community rallies around a single person, but our city loves Buck, what he stands for and his indomitable spirit.
"Buck O'Neil is a man who has done more than anyone to popularize and keep alive the history of the Negro Leagues."
In the months that followed, O'Neil embarked on an exhausting schedule that had him flying to California, Ohio, Arizona and New York among other stops. He spoke at the induction ceremonies in Cooperstown. In July, he batted in the top and bottom of the first inning of the Northern League All-Star game, making him the oldest man ever to play in a professional baseball game.
It was shortly after that when he was first hospitalized.
He was especially loved by the very young. In appearances at children's clubs and elementary schools throughout the country, kids of all color would gather 'round to hear the merry-eyed, grandfatherly figure spin his tales.
Among older African-Americans, however, he would sometimes run into resentment. Why relive the Jim Crow past? Why dredge up bitter memories of segregated lunch counters and public facilities with insulting "whites only" signs?
But O'Neil would fire right back.
"It's very important that we know our history. We have to do that," he said. "I would remind them of a time when baseball was a source of joy for them. Then as we talked about it, they would remember who they were with, even what they wore to the games.
"I would tell them this is not a sad story. It's a celebration!"
In the forward to O'Neil's autobiography in 1996, Burns wrote of his amazing ability to see the goodness in his fellow man.
"His life reflects the past and contains many of the bitter experiences that our country reserved for men of his color, but there is no bitterness in him," he said.
"It's not so much that he put that suffering behind him as that he has brought gold and light out of bitterness and despair, loneliness and suffering. He knows he can go farther with generosity and kindness than with anger and hate."
O'Neil has no children; his closest living relative is a brother, Warren O'Neil.