The Clever Boys were taking the initiative to attack in the early stages of the match while Siwelele were absorbing the pressure and hoping to hit on a counter-attack.
Amr Gamal had the first real opportunity of the match in the 17th minute with a glancing header at the near post following a corner but his effort went across the face of goal.
The visitors had a scare in the 26th minute as a scrambling ball inside the box hit the inside of the post, while Gamal and Daylon Claasen failed to convert the rebound.
Gavin Hunt's charges continued to probe after 38 minutes but they could not create clear goalscoring chances, while Veselin Jelusic's troops were sizing them up from the back and chose their moments when going forward.
However, Phunya Sele Sele increased their tempo in attack in the last five minutes of the half and kept Hunt's men under pressure with Darren Keet comfortably swallowing Ndumiso Mabena's strike inside the box as the first stanza ended goalless.
Gamal had another opportunity in the 55th minute after a pin-point cross from Sifiso Hlanti but his header went straight into the hands of Patrick Tignyemb.
Victor Letsoalo almost broke the deadlock on the hour-mark with a looping header from the edge of the box that could not find the back of the net only because of Keet's desperate fingertips that pushed it onto the under-side of the bar and back into play.
Siwelele were coming out of their shell after 70 minutes with a good spell of possession in the attacking third.
Tignyemb brilliantly saved Gamal's half-volley from the edge of the box in the 76th minute after the Egyptian striker used his body well to turn and shoot.
Hlanti had a good crack at goal with five minutes remaining on the clock with a free-kick on the edge of the box but it sailed over the crossbar.
Vincent Pule snatched the winner with a moment of brilliance, scoring with an exquisite back-heel in the 90th minute after he was set up by Gamal.