Pirates join Moroka Swallows, Bay United, Free State Stars, SuperSport United, Bloemfontein Celtic, Ajax Cape Town and Golden Arrows in the draw for the quarterfinals, which will be conducted in Johannesburg on Monday.
Thanda were boosted by the presence of Bernard Parker and Felix Obada, who both returned early from trials in Europe and were selected in a very attacking line-up by coach Roger Palmgren.
Pirates on the other hand, had only one genuine forward in their match-day 18, the Zimbabwean Gilbert Mushangazhike, who was left to battle the hosts' defence alone in a 4-5-1 formation.
Thanda had the first genuine effort at goal early on, with Nkosinathi Nhleko firing a powerful drive just over the crossbar in the third minute.
Pirates' playmaker Teko Modise should have made more of an opportunity in the 17th minute after Benson Mhlongo had set him up with a header, but the 25-year-old was unable to get on the end of the bouncing ball.
Just a minute later Moeneeb Josephs was called into action, keeping out Obada's powerful volley from a tight angle, and the goalkeeper was lucky that his defenders got the loose ball before any of Thanda's attackers.
Just before half time Pirates' Thulasizwe Mbuyane missed a glorious chance, fluffing his shot from just two metres out after Dikgang Mabalane had used his pace to get to the by-line and set up the former Free State Stars midfielder with a superb cut-back.
Mushangazhike missed a good chance to break the deadlock early in the second half, heading wide under no pressure after Mabalane had again got himself to the by-line and provided an inviting cross for the striker.
Thanda goalkeeper Aubrey Mathibe had hardly had a save to make despite Pirates' dominance of possession, though he was almost caught out just before the hour mark by a long range effort from Lebogang Mothibantwa that took an awkward bounce.
In the 62nd minute Mathibe was finally required to make a good save, palming away Mbuyane's shot after the midfielder had cut inside from the left flank.
On 66 minutes Pirates found the breakthrough. Lucas Thwala charged down an attempted clearance by Thanda defender Siyabonga Mfeka and the bell fell kindly for Mothibantwa, who calmly placed his shot into the bottom corner of the net.
The Buccaneers should have moved two clear four minutes later but Benson Mhlongo couldn't direct his header on target after rising highest to meet a corner kick.
Pirates had a late scare when Ghanaian defender Ahmed Mohammed got on the end of a corner kick, but the Thanda centre-back was unable to hit the target with his header.