The result means Chelsea have become the first club to win two consecutive away games against Hearts of Oak and the Porcupine Warriors.
Kofi Owusu's early goal gave Berekum Chelsea 1-0 victory in a scrappy encounter at the Baba Yara stadium on Sunday.
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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.