Despite their victory in the Soweto derby, Pirates went with four changes as Thulani Hlatshwayo, Bongani Sam, Ben Motshwari and Vincent Pule dropped out.
Pirates felt the pressure in the first five minutes when a first-time curler from Knox Mutizwa following a lay-off from Knox Mutizwa forced goalkeeper Richard Ofori to steer behind for a corner-kick.
However, the Buccaneers sprung to life closer to the half-hour mark as a looping header from Paseka Mako off a cross from the right-side by Deon Hotto forced a save from Sifiso Mlungwana.
Abafana Besthende however went ahead in the last five minutes of the first half through a low finish from a tight angle by Pule Mmodi with the Buccaneers caught napping from a quick throw-in.
The second half started with a double substitution from the Buccaneers, who introduced Motshwari for the injured Ntsikelelo Nyauza and Gabadinho Mhango for Azola Tshobeni.
Pirates were given a penalty 15 minutes after the restart when Lindokuhle Mtshali handled in the area, but Thembinkosi Lorch failed to work Mlungwana with a wayward strike from the spot.
It was duly punished midway in the second half when Mmodi ran in behind the defence from a ball over the top to beat Ofori with a low finish for his brace.
Abafana Besthende began to drop deep to preserve their lead late on, but still found openings to go further ahead however failed to capitalise.
The Buccaneers on the other hand struggled to get going, with Mhango left frustrated up top as Arrows went on to claim victory to leapforg Bucs into fourth spot.