Pirates started off having won two of their last four matches in all competitions, while Horoya hoped for another local scalp after eliminating Mamelodi Sundowns in the group stages last year.
The Buccaneers made a single change from their previous showing at FC Platinum, with Augustine Mulenga replacing Marshall Munetsi while Horoya gave a debut to Abdoulaye Keita in goal.
While the opening 20 minutes failed to provide goal-mouth action, Pirates missed a good chance when Kudakwashe Mahachi set-up Thembinkosi Lorch, who rattled the top of the crossbar on 27 minutes.
The Buccaneers continued with the relentless pressure after Mulenga stormed forward and beat one defender before seeing his shot saved by the finger-tips of Keita two minutes later.
On the stroke of halftime, Lorch showed good composure inside the box to smash the ball into the roof of the net with a left-footed strike for a halftime lead.
Just before the hour, Vincent Pule was unleashed from the dugout to intensify this great desire, before Alfred Ndengane nearly headed the call but his snap-shot from a corner went straight to Keita.
The Sea Robbers eventually registered their second goal after poor communication allowed Shonga to unleash a snap-shot past an advancing Keita that rolled safely into the back of the net.
Inside the final 15 minutes, Shonga completed his double from poor defending yet again when he fed off a poor defensive clearance to find the top of the net.
The hapless Guineans didn’t surrender and continued the fight, but nothing fell their way in the end as Bucs head into match day three as the group leaders ahead of holders Esperance.
Pirates resume duty on the domestic front in midweek with Baroka FC coming to town.
Unused subs: Mpontshane, Makola, Munetsi, Gabuza.