After a 0-0 result at home, the Clever Boys needed to score in Alexandria and showed their intent in the early stages until they went behind via the penalty spot in the 37th minute.
Ben Motshwari was adjudged to have handled in the area after the ball struck him on the shoulder, and Ahmed Mekki sent Moeneeb Josephs the wrong way from 12 yards.
Wits coach Gavin Hunt brought on Mogakolodi Ngele for Phakamani Mahlambi at the start of the second half, while Cuthbert Malajila replaced Eleazar Rodgers with 20 minutes remaining.
Neither substitution managed to help affect the scoreline as Wits resorted to long balls in the final few minutes, to no avail as the Egyptians held firm at the back while playing on the counter-attack.
Bidvest Wits: Josephs, Gaxa, Khumalo, Ntshangase, Frosler, Motshwari, Pule, Myeni, Mhango, Mahlambi (Ngele 46'), Rodgers (Malajila 71')