Clif Smart, the university's interim president, said the selection of the tune, which is associated with the Confederacy, was "unfortunate" and would be stricken from the MSU Pride Band playlist.
"I have personally apologized," Smart said. "That selection will not be played again in a public venue."
While it may be catchy, "Dixie" took on a negative connotation among a number of complaints to the Springfield NAACP.
"It wasn't so much the history of the square," said chapter president Cheryl Clay. "It is not an appropriate song that should be played."
The venue was Park Central Square where three African-Americans were hanged at the height of Jim Crow, the Springfield News-Leader said.
Smart told the newspaper he had spoken to the band director, who also expressed his regrets. "He didn't truly understand the significance of the song in relation to the square," Smart said. "He is very sorry about the selection."