Kurt Lentjies had the first chance at the Harry Gwala Stadium; his long-range free-kick forcing goalkeeper Thabani Stemmer into a smart save.
On 33 minutes, a quick Celtic counter-attack saw Lennox Bacela bare down on Francis Chansa, but the keeper did well to block his shot.
Just after the restart Thabo Nthethe came to the rescue for Celtic, saving the blushes of his keeper, who had spilt a cross with a host of attackers around.
Bacela wasted two more good chances, while Lentjies also squandered a glorious opportunity when he found himself unmarked in the box.
Chansa then did well to palm away a Nthethe effort, while Mulenga missed a chance of note when he made a run into the box, but then sent his left-footed shot wide.
So after a goalless 90 minutes, it took just second for Maritzburg to take the lead when substitute Ncubeni powered the ball into the back of the net.
Celtic had a efforts, but Sibisi made sure his side progressed to the last 16 when he slotted home from eight yards out.
Celtic hearts sunk further as Diyo Sibisi made the lead 2-0 as he slotted the ball into the back of the net from the 8-yard area to eliminate Celtic once more.
Maritzburg: Chansa, Evans, Diouf, Matuka, Lentjies, Booysen, Matle (Ncubeni 65th), Obada (Poggenpoel 112th), Morton, Olomu (Madondo 73rd), Sibisi
Celtic: Stemmer, Moleko, Mahoa, Nthethe, Motlhaping, Mkhwanazi, Madubanya, Venter (Mongala 70th), Mulenga, Oerson (Leonard 75th), Bacela (Ortorugu 98th)