He was born in Caracas, Venezuela. He was born to Sephardic Jewish parents from Morocco and Algiers. Benacerraf's brother is Paul Benacerraf, a well-known philosopher. His father was a textile merchant. In 1925, he moved from Venezuela to Paris. In 1940, after he went back to Venezuela, he emigrated to the U.S.. He earned his B.S. at Columbia University School of General Studies in 1942. Benacerraf later went to the Medical College of Virginia where he earned his Doctor of Medicine degree.