Recreativo progressed through to the competition first round stages with a 4-2 aggregate score, having won the first leg 3-1 in Port Elizabeth a fortnight ago.
The hosts took the lead against the run of play at the 5 000-seat Patrice Lumumba Stadium, courtesy of captain Maieco Henrique's 34th minute near post header.
The Angolan international forward netted a brace in the first leg last month.
Pirates equalised on the stroke of half-time through Andile Jali, who drilled a shot past goalkeeper Lando, for a 1-1 interval score.
However, the first-half goal from the hosts had diminished Pirates' already slim hopes of reversing the shock score from two weeks ago.
The South Africans entered the fray needing three unanswered goals to start off a miracle comeback win.
Pirates started off the fixture at a frantic pace in the opening quarter of the match, but drew a first save from goalkeeper Lando in the 23rd minute through striker Bongani Ndulula.
They dominated possession in the encounter while Recreativo remained calm and seemed happier to absorb the pressure from their desperate opponents.
In his starting line up, the Buccaneers coach Julio Leal opted to leave out skipper Lucky Lekgwathi, striker Benni McCarthy and Daine Klate.
Goalkeeper and captain-of-the-day Moeneeb Josephs made the starting line-up with Senzo Meyiwa having stood in goals the last time these sides clashed.
In the second-half, the ineffective Ndulula was replaced by Tokelo Rantie after 50 minutes as Pirates went for a late surge to win the encounter.
A minute later, the busy Mabalane fashioned a long range free-kick that was stopped by Lando.
Recreativo pressed forward on a rare counter-attack soon after with striker Henry Camara finding the side netting.
McCarthy was introduced for Mabalane on the hour mark as Pirates again upped their tempo with Tlou Segolela drawing a splendid save from Lando in the 63rd minute.
They "netted" in 71st minute through Siyabonga Sangweni from a Oupa Manyisa cross, but McCarthy was adjudged to have been offside by the match officials.
McCarthy manuevered a powerful shot from distance that tested Lando in the 76th minute.
Late efforts from Sangweni and Thulasizwe Mbuyane went astray, as did the African ambitions of the expensively-assembled Premier Soccer League outfit.