The South African outfit fell behind to Hugues Zagbayou's opener at the Dobsonville Stadium on Sunday before it looked as though Matthew Rusike's 86th-minute strike had rescued a draw.
However, there was more drama as Koffi Davy Boua scored in the second minute of injury time to leave the Ivorian side in a healthy position ahead of the next week's return leg, leaving the Kaizer Chiefs' hopes of reaching the group stages in the balance.
Cotonsport still have work to do in their tie with Angolan side Petro de Luanda, but the Cameroonians do take a 2-1 lead into the second leg thanks to Carlain Manga Mbah's decisive goal in the 75th minute.
Leopards de Dolisie - champions in 2012 - put one foot in the group stages after the Congo side triumphed 2-0 over Ghanaian outfit Medeama at the Stade Municipal Denis Sassou N'Guesso.
Sewe Sport of the Ivory Coast are also in a promising position as Roger Assale scored at the end of each half in a 2-0 home victory over Bayelsa United of Nigeria.
Elsewhere, Horoya of Guinea were held to a 0-0 draw at home to Tunisian outfit Etoile Sahel, while Abdallah Said's solitary strike was enough for Egyptian outfit Al Ahly to take a first-leg lead over Moroccan side Difaa El Jadida.
In the battle between two Mali teams, Real Bamako will take a slender advantage to Djoliba, after emerging with a 2-1 win.
