Pirates dominated the opening minutes of the encounter, hogging all the ball possession and getting in a couple of shots from range, all of which went wide, as the Cape side struggled with the pace of the game early on.
Having survived a couple of shaky moments at the back, the home side finally provided some threat of their own around the quarter hour mark as Zaakir Williams powered a header over goal before Tyren Arendse's rising first time effort cleared the crossbar.
Santos seemed to be playing themselves back into the game, but a reckless challenge by Sachin Dawood on Tlou Segolela gave the visiting team a penalty.
Lennox Bacela easily sent Pa Dembo Touray the wrong way to give Pirates a 1-0 lead on the half hour mark.
Santos did their best to get back into the game and were close to levelling matters just before the break, but Tshepo Mabua was unable to capitalise on some sloppy defence in the Pirates box.
After the break the Sea Robbers looked to slow the game down, trying to take the sting out of any possible comeback from the hosts as they maintained possession and sprayed the ball around.
The pressure paid off on 65 minutes as the Soweto giants increased their lead to two after Rooi Mahamutsa scored with a header from Mpho Makola's corner kick.
There was a rare chance for the Peoples' Team on 70 minutes, but former Kaizer Chiefs striker David Radebe' shot from 25-metres whistle just wide of the target.
Pirates had a couple of late scares as Lucky Lekgwathi gave away a penalty for a hand-ball in added time, but Senzo Meyiwa made an excellent stop to keep out Radebe, and followed up with a lob in the dying seconds bouncing off the crossbar as Bucs closed out the game 2-0.