Gwynn had two operations for cancer in his right cheek between August 2010 and February 2012. The second surgery was complicated, with surgeons removing a facial nerve because it was intertwined with a tumor inside his right cheek. They grafted a nerve from Gwynn's neck to help him eventually regain facial movement.
Gwynn had said he believed the cancer was from chewing tobacco.
Gwynn had been in and out of the hospital and had spent time in a rehab facility, Boggs said.
"For more than 30 years, Tony Gwynn was a source of universal goodwill in the national pastime, and he will be deeply missed by the many people he touched," Commissioner Bud Selig said.
Gwynn was last with his San Diego State team on March 25 before beginning a leave of absence. His Aztecs rallied around a Gwynn bobblehead doll they would set near the bat rack during games, winning the Mountain West Conference tournament and advancing to the NCAA regionals.
Last week, SDSU announced it was extending Gwynn's contract one season.
San Francisco Giants third base coach Tim Flannery, who played with Gwynn and then coached him with the Padres, said he'll "remember the cackle to his laugh. He was always laughing, always talking, always happy."
"The baseball world is going to miss one of the greats, and the world itself is going to miss one of the great men of mankind," Flannery said. "He cared so much for other people. He had a work ethic unlike anybody else, and had a childlike demeanor of playing the game just because he loved it so much."
Gwynn played in the Padres' only two World Series and was a 15-time All-Star.
He homered off the facade at Yankee Stadium off San Diego native David Wells in Game 1 of the 1998 World Series and scored the winning run in the 1994 All-Star Game. He was hitting .394 when a players' strike ended the 1994 season, denying him a shot at becoming the first player to hit .400 since San Diego native Ted Williams hit .406 in 1941.