Relebohile Mofokeng was the star of the show for the Buccaneers as the Bafana forward scored a goal and provided an assist in the contest.
The Soweto giants started the game well and were rewarded in the 16th minute when Mofokeng headed them into the lead following a fine cross from Tshepang Moremi.
Usuthu almost found equaliser immediately after conceding but Keegan Allan was denied by Pirates goalkeeper Sipho Chaine.
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Amazulu shot-stopper Darren Johnson was kept busy, making saves to deny Deon Hotto, Thalente Mbatha and Oswin Appollis towards the end of the first half.
Pirates did not have the same fluency after the interval and the home team were starting to get a whiff of getting back into the contest.
Usuthu had a golden opportunity to level the score with six minites remaining but Chaine again came out on top, saving an effort from Langelihle Mhlongo.
Pirates secured all three points in stoppage-time when Mofokeng’s shot hit the post but went into the net off the unfortunate Johnson.
The Soweto giants will prepare for a Nedbank Cup clash against Tshakhuma Tsha Madzivhandila on Saturday while Amazulu take on Polokwane City in the knockout tournament on 10 February.