Khalifa was chosen by the Pittsburgh Pirates as the seventh overall selection in the 1982 Major League Baseball Draft. Though he signed a letter of intent to attend Arizona State University, Khalifa signed with the Pirates, receiving a $100,000 signing bonus. In 1982, he played for the Gulf Coast Pirates of the Rookie-level Gulf Coast League (GCL) and the Greenwood Pirates of the Class A South Atlantic League. In 48 games played for Greenwood, Khalifa had a .305 batting average. He played six games for the GCL Pirates. In 1983, he played for the Alexandria Dukes of the Class A Carolina League and made the All Star team, batting .270 in 103 games, and received five games of playing time for the Lynn Sailors of the Class AA Eastern League.