The Frenchman will succeed Juergen Steinemann, who has headed the firm since 2009, on October 1, the company said.
Steinemann had announced last year that he would step down, citing family reasons.
He will however remain vice-president of Barry Calleabaut's board, a post he was elected to in December.
"With Antoine de Saint-Affrique, the board has appointed a new CEO with an impressive track record in the food industry," the company said in a news release.
“I am honoured to be given the opportunity to lead and further shape the world's leading chocolate and cocoa company as its CEO," Saint Affrique said in a statement.
"Barry Callebaut offers a unique environment since it combines three qualities which rarely come together: a global leader, which is publicly listed, but also a family company with longer-term purpose, vision and a strong entrepreneurial spirit.”
Born in 1964, Saint-Affrique has held a series of top jobs in the food sector.
Apart from being Unilever Foods head, he is also a non-executive director of Essilor, a leading lens-maker.