Bakgaga came with unchanged eleven from their semi-final win over Bidvest Wits, while Bucs made one change from the side that got the better of Kaizer Chiefs.
The Bucs technical team was left fuming after Thembinkosi Lorch went through on goal following a defensive error and he failed to make it count as he shot straight at Elvis Chipezeze.
Baroka started with confidence and attacked with pace, but their final delivery was what let them down in trying to supersede the Ghost.
Pirates though were the more adventurous despite failing to test Chipezeze. The defensive block from Baroka meant that Vincent Pule and Justin Shonga could only take shots from range.
Pule was causing all the problems with his pace out on the right, as he got under neat a long ball before turning a defender for a left-foot curler but it went over the top.
Baroka’s rare moment in attack saw Talent Chawapihwa pulling a cut back into the box to have a shot at goal, but the Bucs defence stood well in line to block it from finding the target.
A studs-up challenge by Marshall Munetsi on Vusi Sibiya gave referee Victor Gomes no choice but to hand him a straight red card to leave Bucs with 10 men for the rest of the match.
Baroka took the lead to much jubilation when Jemondre Dickens lashed home a nice lay-off into the top corner following an error from Siyabonga Mpontshane
Having their backs against the wall, the Buccaneers squirmed a big chance to draw level a minute from returning from the break through Xola Mlambo on the edge of the box.
Just as well, Tebogo Sodi expertly brought down a long ball from defence to nutmeg Happy Jele and go face-to-face with Mpontshane but the final effort was woefully wasted.
Chipezeze’s first save came after Musa Nyatama played in Shonga inside the box which the Zimbabwean international managed to palm into touch.
Bucs were level soon after when Nyatama’s instant reaction guided him to pounce on a loose ball off a Shonga free-kick for a first-time finish.
Baroka made their first change, with Dickens coming off for Botswana international Onkgebatse Makgantai in the final quarter.
The Sea Robbers missed a good chance to go in front, but Augustine Mulenga failed to tuck in a cross-field pass from Lorch with a wayward execution.
Following good hold up play from Mulenga, Pule availed himself for a shot but Chipezeze’s outstretched hand kept it from finding the net.
It was Chipezeze denying them again as he directed Shonga’s snap shot inside the box for a corner as the game headed into extra time.
After a pacey start to the next 30 minutes, Bakgaga were handed a penalty when Mduduzi Mdantsane played in Makgantai who danced past the defence to be brought down by Mpontshane.
The lead was restored as Mdantsane blasted home with his left-foot into the bottom corner, giving Mpontshane no chance.
Bucs were still running as ever, and a shot from a corner by Thabiso Kutumela was largely their only threat to grabbing the equaliser for the second time in the contest.
Bucs pulled another rabbit out the bag after Lorch sneaked in at the far post to beat Chipezeze in the bottom corner with a low header after a pin-point cross from Shonga.
The woodwork came to Baroka’s rescue later on when a half-hearted attempted from a corner found the head of Shonga who onto the post of Chipezeze, as penalties happened.
After comfortable first conversions, both sides missed their respective seconds before Kutumela missed the fourth with Davies Nkausu following suit.
However, Lorch was unable to capitalise thus allowing Bakgaga to clinch their maiden cup title in the PSL era.
Baroka: Chipezeze, Mabeba (Makgaka 79'), Makume, Gebhardt, Mdantsane, Sodi (Nkausu 104'), Mosele, Chawaphiwa, Semenya, Dickens (Makgantai69'), Sibiya.
Subs: Dlamini, Kgoetyane, Chivaviro, Makgaka, Nkausu, Kgaswane, Makgantai.
Pirates: Mpontshane, Jele, Munetsi, Mbekile(Qalinge 102'), Maela, Nyatama, Mlambo, Pule (Mako88'), Lorch, Shonga, Mulenga (Kutumela 102').
Subs: Mabokgwane, Da Silva, Mako, Makola, Mntambo, Qalinge, Kutumela.