The Buccaneers, who seemed unstoppable a few weeks ago, saw their unbeaten run in regulation time in 27 matches across all competitions come to an end.
Goal takes a look at what caused Bucs' sudden collapse.
Milutin 'Micho' Sredojevic made two changes to the team that faced and drew with Kaizer Chefs in a massive Premier Soccer League (PSL) encounter.
Paseka Mako and Linda Mntambo surprisingly made their return to the starting line-up ahead of Pirates' toughest away fixture in the group stage.
This was at the expense of Xola Mlambo and Justin Shonga, who have established themselves as influential players in the Bucs squad since last season.
Midfielders Mako and Mntambo struggled to stamp their authority as the Blood and Gold dominated the midfield battle which set the tone for the hosts' victory.
It was quite clear that Bucs were missing the influence of midfield talisman Mlambo, who had started alongside Ben Motshwari and Musa Nyatama against Chiefs in a 4-3-3 formation.
Micho should have stuck with the three midfielders which would have enabled Bucs to match the Tunisian champions, who were expected to adopt an offensive approach at home.
Mlambo watched on from the bench as an unused substitute, while Shonga came on just after the hour-mark with his side chasing the game.
However, the 1995 Champions League winners could not create enough chances to win the match or let alone snatch a late draw.
Micho's tendency to make unnecessary changes to the starting line-up seems to be hurting the team in recent weeks with the Soweto giants now winless in their last five games.
Shonga, Augustine Mulenga, Vincent Pule and Thembinkosi Lorch have formed one of the deadliest attacking units in the country and they have been key in Bucs' quest for PSL and continental glory.
The decision to start one of the four attackers from the bench and introduce them in an effort to change the complexion of the game has proved costly.
Lorch and Mulenga were brought on as substitutes against Baroka FC and Chiefs respectively with Bucs trailing and they helped the team secure draws.
Unfortunately, dropping points has seen the Soweto giants slip down the PSL log from second spot to third place after failing to secure maximum points.
The decision has now backfired in the Champions League as Bucs are now placed third on the Group B standings with two important matches left.
It is now imperative for Micho and his technical team not to make unnecessary changes to his starting line-up as Pirates approach the home stretch of the current season.