The Hall of Famer and three-time Most Valuable Player died of "natural causes" late Tuesday, the museum said in a statement.
"Yogi conducted his life with unwavering integrity, humility and a contagious good humor that elevated him from baseball legend to beloved national icon," the museum said.
Berra, a 15-time All Star and 10-time World Series champion, was inducted into the Hall of Fame in 1972.
But the baseball great was equally well-known for humorous quips and malapropisms such as "It's deja vu all over again."
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Major League Baseball columnist Marty Noble said on the league's online news page that "a loss that unquestionably transcends the game has sent all of baseball into deep mourning."
Berra's museum announced his death "with a profound sense of loss and heartfelt sorrow."
His family added that "while we mourn the loss of our father, grandfather and great-grandfather, we know he is at peace with mom."
Berra, whose real first name was Lawrence, was born in St Louis, Missouri in 1925 to Italian immigrant parents from Milan.