The hosts got off to a brilliant start and opened the scoring in the second minute when Manyisa collected a pass from Mbesuma near the centreline and raced towards box before slotting the ball past Ronwen Williams.
Two minutes later Franklin Cale tried a snapshot from just outside the penalty area but he failed to get his bearings right and sent his volley over the crossbar.
Then in the ninth minute the Buccaneers should have doubled their lead when Davies Nkausu flicked the ball towards Daine Klate, but his volleyed effort clipped the top of the crossbar.
The rest of the half saw Matsatsantsa pinning Pirates in their own half with the use of long balls, but they failed to cause real problems for the defence and goalkeeper Senzo Meyiwa.
Roger De Sa’s men had a chance to double their lead six mintes before the break as Klate cut the ball back towards Sifiso Myeni just outside the box, but he pulled his shot wide of the far post.
The second half started at a frantic pace with SuperSport committing men forward in search of the equaliser.
However, it was the hosts who came close to extending their lead in the 50th minute when Happy Jele found Klate at the far post but Williams reacted quickly to stop his looping shot on the line.
Then three minutes later Simba Sithole should have leveled matters when a cross from Edwin Gyimah found him unmarked inside the box, but he directed his header over the crossbar from point-blank range.
Gyimah tried to take matters into his own hands in the 60th minute as he tried to place his volleyed shot in the top right corner, but the ball dipped over the crossbar before clipping the top netting
Then in the 72nd minute the home side were handed a golden chance to double their advantage when they were awarded a penalty as Klate was brought down by Davies Nkausu, although it looked like the infringement had happened just outside of the box.
Andile Jali stepped up to take the spotkick but Williams dived low to his right to keep his effort out, giving his side a chance to get back into the game.