He spent eight seasons in the Braves' farm system in the still-segregated Deep South, during which he wrote poetry concerning baseball and racism.

Due to the presence of longtime All-Star Eddie Mathews at third base, the Braves traded Charles to the Kansas City Athletics prior to the 1962 season with Joe Azcue and Manny Jiménez for Lou Klimchock and Bob Shaw.

In 1969, he shared third base duties with rookie Wayne Garrett as a member of the Miracle Mets team that unexpectedly won the World Series, after finishing dead last in five of its first seven seasons and 9th in a 10-team National League in the other two.

On September 24, they clinched the division with a 6–0 victory over the St. Louis Cardinals, with Charles homering off Steve Carlton (his final Major League home run) and Donn Clendenon homering twice and Gary Gentry pitching a four-hitter for the victory.

Charles played in four of the five games in the World Series, in which the Mets defeated the heavily favored Baltimore Orioles.