Pule Mmodi got at the end of a long goal kick from Bruce Bvuma to beat Free Agents goalkeeper Ugonna Igidimba and hand Kaizer Chefs the lead after 18 minutes.
Eight minutes later, Mmodi was back and this time finished a slick pass from Wandile Duba to make life difficult for Free Agents who were formed in 2018.
The Soweto giants then deflated their third-division opponents when defender Inacio Miguel headed in to make it 3-0 for Chiefs in the 62nd minute.
As Free Agents protested that Miguel had scored from an offside position, they were brought to a man down when Saheed Adebayo was red-carded.
Some shambolic marking by Free Sgents defenders allowed an unmarked Ranga Chivaviro to score Chiefs fourth goal with seven minutes to full time and that assured security for Amakhosi.
It was an important victory for Chiefs who have been eliminated from this competition by lower-division sides seven times before.