Chiefs travelled to the Ivory Coast with a squad of only 13 players and placed assistant coach Doctor Khumalo in charge as Stuart Baxter remained at home to prepare for his side's next League match.
There were not many changes to the starting eleven that lost 2-1 in the first leg at home as Morgan Gould captained the side.
ASEC had an early penalty appeal waved away in an open start to the game before Rusike rattled the woodwork in a show of intent. Chiefs' fringe players looked hungry to impress in the heat of Abidjan.
However, despite the Ivorian side showing their visitors respect, Chiefs were unable to break down a stubborn ASEC defence and failed to register many shots on target in the first half.
In the second half ASEC striker Foba Stevens Koffi went close with one effort and sent another shot wide as he looked to break the deadlock.
Khumalo eventually used one of his two substitutes named on the bench when Lorenzo Gordinho came on for Siyabonga Nkosi, who was dictating the play in the first half.
It was a game short of goalmouth action as Chiefs had 10 goal attempts but were unable to make the ASEC goalkeeper work, while Reyaad Pieterse was also having a quiet day at the office.
However, Koffi got the goal he was looking for late in the game after receiving the ball in the six-yard area and placing a shot past Pieterse. The linesman had his flag up as he scored, but the referee awarded the goal.
The goal ended the tie as Chiefs lost 3-1 on aggregate and were knocked out of Africa.
Chiefs XI: Pieterse, Moleko, Mtsweni, Gould (c), Bukenya, Baloyi, Maluleka, Cele, Nkosi (Gordinho 70'), Rusike, Masango
Bench: Khuzwayo, Gordinho
Coach: Doctor Khumalo