Youngster Theophilous Okoe underlined his fox-in-the-box tag when he popped up to head home from an Ekow Benson spilled free-kick in the 16th minute.
Joseph Bentil was left unmarked just outside of the area and he punished the Blues by smashing home to cushion the lead for the home side.
New signing Evans Obeng climbed off the bench to halve the deficit for the Chelsea.
The Habour Boys had ex-Ghana international Ekow Benson in their line-up and it was his influence that led to the opener. Benson darted a powerful drive at goal which was spilled by the Chelsea keeper and Okoe arrived in time to head home.
Youth perpetuated their dominance in midfield and continued to threaten the Chelsea halve of the pitch.
Chelsea also had their chances but former Liberty Professionals and Bofoakwa Tano striker Yaw Antwi fluffed his lines. However 19-year-old Evans Obeng was introduced in his place and the budding talent scored on his debut in the Ghanaian top-flight.
The former Berekum Arsenal attacking midfielder wriggled his way round to finish off for his first ever goal in the Ghanaian top-flight.