The Soweto giants were carrying a 5-1 aggregate lead going into the return leg clash having secured a commanding victory at home in the first-leg clash.
Milutin Sredojevic made three changes to the team that faced Stars at the Orlando Stadium with Linda Mntambo starting alongside stand-in captain Mpho Makola midfield.
The Buccaneers were clear favorites to win the match against the reigning Seychelles League Cup winners in the Praslin island.
It took only 11 minutes for the visitors to break the deadlock after the hosts' defence was exposed and it was Mntambo, who scored to opened the scoring.
Mntambo combined with Zimbabwean winger Kudakwashe Mahachi, before hitting the back of the net to make it 1-0 to Pirates.
The former Jomo Cosmos captain had also found the back of the net for 1995 Caf Champions League winners in the first-leg encounter.
The goal did not come as a surprise as Bucs had scored 12.5% of their goals in the first 15 minutes of the game in the league this season.
The two teams then struggled to create goalscoring opportunities with much of the play concentrated in the middle of the park.
There was no supply for returning striker Thamsanqa Gabuza, who was making his first competitive appearance for Bucs since August 2018.
The former Lamontville Golden Arrows marksman was hoping to end his scoring drought having last netted for Bucs seven months ago.
Pirates were able to on hold to their slender lead and they were leading 1-0 at the interval and 6-1 on aggregate.
An entertaining second half followed as the Buccaneers piled pressure on Stars and they created chances which they converted.
Pirates managed to double their lead on the hour-mark and it was Gabuza, who scored to make it 2-0 to the visitors - ending his goal drought in the process.
The momentum was with the four-time PSL champions with Gabuza keeping the Stars defence with his movement around the hosts' box.
It was soon 3-0 to Pirates when Gabuza's shot was fumbled and Abel Mabaso reacted quickly, and hit the back of the net.
The defender-come-midfielder, who joined Bucs from Chippa United ahead of the current season, had grabbed his maiden goal for the club.
Stars pushed for a late consolation goal and they managed to find the back of the net to make it 3-1 in the latter stages of the game.
Sredojevic then pulled off Mahachi and he introduced defensive-minded Asavela Mbekile as the Buccaneers looked to hold to their two-goal lead.
Ultimately, Pirates ran out 3-1 winners over Stars after containing the hosts in the dying minutes of the encounter.
The victory saw Bucs advance to the first round after winning the tie 8-2 on aggregate, while Stars bowed out of the tournament.
Pirates will take on either Namibian side African Stars or Volcan Club of Comoros in the next round.