Cape Town - A 1-0 defeat to Smouha at the Borg el-Arab Stadium on Saturday evening saw Wits eliminated from the 2017 CAF Confederation Cup.
Despite enjoying good passages of play in both halves, Gavin Hunt's side lacked a cutting edge in attack while Smouha were happy to play on the counter and to sit back and defend their lead after scoring.
Following last weekend's 0-0 draw in Johannesburg in the first leg, the Students started the game strongly and had the Egyptian outfit on the back foot for much of the opening 30 minutes.
But having failed to turn their dominance into clear-cut chances on goal, Wits found themselves 1-0 down just after the half-hour mark.
The goal came via a penalty from Egypt international Ahmed Mekky, the spot kick awarded after the ball was deemed to have struck Ben Motshwari on the arm, in what seemed a harsh decision.
The second half saw the Clever Boys making a positive start as they came out looking for the equaliser.
But apart from a well-hit long-range shot on the hour mark by Siboniso Gaxa which drew a superb save out of the home keeper, they were unable to prise open the home defence.
The visitors kept pressing right till the end, but Smouha were able to successfully shut up shop to book their spot in the group phase, while Wits return home to continue their challenge for domestic title honours.