The Porcupine Warriors stun the host by taking a two-goal lead in the opening 30 minutes.
Emmanuel Gyamfi scored first with a composed finish in the 10th minute before Maxwell Baakoh struck a stunning effort from the edge of the box into Coto Sport net.
Coton Sport managed to pull a goal back four minutes to end of the first half courtesy skipper Kamilou who scored from the penalty spot.
However, five minutes into the second half the two-goal was restored. Abdul Fatawu pounced on a misplaced back pass to score for Kotoko.
Kotoko choose to sit back thereafter with the intention of soaking the pressure and hitting Coton Sport on the counter.
This strategy worked to a large extent until the 70th minute where Kamilou Dauda capitalized on a defensive mishap to score his second of the game.
Coton Sport, buoyed by the home fans went in search of the elusive equalizer by upping the ante up front but Kotoko defended well to claim the win.
The famous victory puts Kotoko in good stead to reach the group stage of Confederation Cup for the first leg in 10 years.
The second leg will take place in Kumasi next weekend.
Watch the HIGHLIGHTS of the game below
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