The result means Chelsea have become the first club to win two consecutive away games against Hearts of Oak and the Porcupine Warriors.
Owusu netted in the 7th minute, thumping in as the ball broke loose following Jeorge Renchi's burst forward.
Kotoko suffered a massive blow in the 76th minute when defender Empem Dacosta was given a second yellow card and a subsequent red for an off-the-ball incident.
Berekum Chelsea managed to see out the game with the man advantage.