Leading 3-2 from the first leg, the Porcupine Warriors wrapped up the tie with two goals before the 60th minute.
Amos Frimpong stayed composed to put Kotoko ahead from the spot on the stroke of halftime after a foul on Burkinabe striker Songne Yacouba before Maxwell Baakoh, who was amongst the goals in Yaoundé last week, doubled the lead in the 53rd minute with a brilliant effort.
The former Karela United left-winger teased the Coton Sport goalkeeper to get off his line before shooting into the far corner.
The Cameroonian side, who reached the Champions League final in 2008, did not lose their spirit and grabbed a consolation goal when Oumarou Sali capitalised on poor marking inside the Kotoko penalty bot to strike into the bottom corner of the left post.
Kotoko have thus achieved their target of reaching the money zone for the for the first time in 11 years.
They were finalists in the maiden edition of the competition in 2004, losing the title to fierce rivals Hearts of Oak.
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