He later apologised for his remarks.
He was also embroiled in a public feud with the African-American Studies department that erupted shortly after he became president in 2001.
Faust also becomes the first president without a Harvard degree since Charles Chauncy, who graduated from Cambridge University, died in office in 1672.
She attended Bryn Mawr College and the University of Pennsylvania, where she was also a professor of Southern history.
The Harvard presidency is one of the most prestigious jobs in US higher education and the university has a budget of $30bn.