The game continued from where they left off yesterday after rains had rendered the Baba Yara pitch unplayable.
It was Guinean international, Naby Keita who converted from the spot during additional time after Songne Yacouba was brought down in the penalty box.
Kotoko coach, Kjetil Zachariassen named an unchanged lineup from yesterday as the match began from the second half.
With South African referee Eugene Nkosinathi Mdlule ruling out Kotoko’s initial goal for an offside, the match appeared to be heading for a draw until forward, Songne Yacouba was brought down during additional time.
Second half substitute, Naby Keita stepped up and converted the resulting kick to give Kotoko a 1-0 lead ahead of the second leg in Ivory Coast.