Substitute Yakubu Mohammed managed to nail it in injury time after three previous spot kicks were squandered by the home side.
Referee Issa SY from Senegal remains the star man for awarding five penalties in a match. The Kumasi giants missed three and scored one while opponents CARA also missed theirs.
His first call was in the sixth minute but striker Saddick Adams hit his effort wide.
)
)
)
From the recess, Kotoko piled pressure on CARA Club and they were awarded with another penalty in the 57th minute, this time Amos Frimpong stepped forward and his kick was saved.
Five minutes later, the referee awarded another penalty for the Kumasi giants after Kwame Boahene was brought down, however, Baba Mahama selected himself to take the kick and he failed to pick his spot.
The visitors had a glorious opportunity to take the lead when they were awarded a penalty but goalkeeper Chansel Massa-who had saved two spot-kicks- missed from 18 yards as his opposite number Felix Annan saved.
The second leg is expected to come off in two weeks time in Congo Brazzaville and both teams will hope there is less drama.