Kaizer Chiefs came into this clash looking to put their opponents to the sword going into the second leg in Ivory Coast next weekend, and they survived a scare as early as in the fifth minute when Koffi Foba's shot went inches wide of Reyaad Pieterse's goal.
AmaKhosi, however, came close to opening the scoring in the 11th minute after Matthew Rusike's shot was parried back into play by Mimosas goalkeeper Sangane Badra Ahi before Mandla Masango failed to hit the target from the rebound.
Mimosas sat back and often played long balls forward, while the home side continued to build from the back, although they were let down by their poor passing in the final third.
Zagbayou Hugues then broke the deadlock in the 36th minute following Chiefs' failure to deal with a long throw-in into their own box, to give the visitors a vital away goal.
Stuart Baxter's side could not recover from that goal as Mimosas held on to their 1-0 lead going into the final 45 minutes of the game.
The Soweto giants introduced Philani Cele for George Lebese before the start of the second half to try and unlock the Mimosas defence with his pace.
Masango forced Badra to a great save from a 54th-minute free-kick, as Chiefs looked to level matters and wrestle the game away from their opponents.
Chiefs piled more pressure on Mimosas and had a chance to grab the equaliser midway through the second half, but the Ivorians cleared their lines.
Matthew Rusike then levelled matters with a beautifully taken goal four minutes from time, much to the relief of the AmaKhosi fans out in the stands.
However, Boha Koffi struck deep in stoppage time to make it 2-1 to the visitors and dent AmaKhosi's hopes of making it to the Caf Confederation Cup group stages.