Captain Itumeleng Khune returned in goal, while Godfrey Walusimbi, Mario Booysen and Teenage Hadebe were given a start by Ernst Middendorp.
Elgeco threatened to get on the front-foot, with a low cross into the box but it went astray after no one was able to make contact with the delivery inside 15 minutes.
Chiefs continued to be washed with strong challenges from the hosts while trying to find a way in behind the defence, as little room opened up for Zuma, Lebohang Manyama and Leonardo Castro.
It was the visitors who started the second half in a positive light despite the limited creation of clear-cut chances on both sides.
There was to be a promising scenario after Hendrick Pule Ekstein opened up space from the midfield to allow Willard Katsande to have a shot from range, but he shot over the top on 60 minutes.
After coming from the bench, Bernard Parker instantly set the wheels in motion by putting Ekstein through to get the opening strike inside 71 minutes.
The Amakhosi were now all but confirmed third round participants, but Bernard Parker wanted to make sure it was the case by attempting a second, however he shot wide of target on 78 minutes.
Following a much-awaited return from injury, Ryan Moon was introduced for Castro inside the final quarter of the match.
The Chiefs forward wasted little time to make his presence felt by heading home the second following a nicely laid delivery eight minutes from time.
With four minutes to go, Ekstein completed proceedings for the Soweto giants by completing his double to hand the Amakhosi a spot in the third round phase on a 6-0 aggregate tally.
Chiefs: Khune, Booysen, Walusimbi, Hadebe, Cardoso, Katsande, Zulu, Manyama, Ntiya-Ntyia, Castro, Zuma.
Subs: Vries, Mahlasela, Parker, Ekstein, Ngezana, Ntshangase, Moon.