Thulasizwe Mbuyane struck in the first minute of injury time to hands Bucs a win which sees them move up to third on the table just two points adrift of leaders Mamelodi Sundowns.
Matsatsantsa, meanwhile, have dropped to just above the relegation zone and have only themselves to blame for this defeat after missing several good chances.
SuperSport handed debuts to new signings Rowen Fernandez and Mario Booysen, while Pirates went for an unusual strike partnership in the shape of Thulasizwe Mbuyane and Patrick Malokase.
On 20 minutes the first chance of the game fell to the hosts, with Lyle Lakay floating in a good cross from deep on the left flank that was headed wide of the target by Fikru Tefera.
The striker had managed to get goal-side of Rooi Mahamutsa, for which the Pirates centre-back was berated by his goalkeeper.
Pirates came close to opening the scoring just a minute later, with Clifford Ngobeni firing a long-range effort just wide of the target after a cleverly-worked free-kick routine.
On 26 minutes Daine Klate had a wonderful chance to score against his former team but, after being put through one-on-one with the goalkeeper, he was denied by a superb, one-handed reaction save from Fernandez.
The former Kaizer Chiefs keeper came up with another excellent save five minutes later, strongly pushing away a shot from Mbuyane after the attacker had cut inside from the left and let fly from the edge of the box.
On 35 minutes United were inches from taking the lead. Anthony Laffor fired a low shot on target that was only half stopped by Moeneeb Josephs – the loose ball rolled toward the goal line but the keeper quickly got up and smothered it.
Just before the hour mark Letladi Madubanya spurned perhaps the game’s clearest chance, mis-controlling after being put through on goal by a clever back-heel from Laffor which allowed Josephs to easily collect the ball.
On 67 minutes Laffor himself almost broke the deadlock, seeing his close-range effort deflected just wide of goal by Happy Jele after he had exchanged passes with substitute Kermit Erasmus.
Seven minutes later Pirates needed skipper Lucky Lekgwathi to clear off his own goal-line after Josephs had flapped at a cross from Thabo September.
Neither side looked prepared to settle for a point as the clock wound down. Pirates created a great chance to score in the 87th minute when substitute Mark Mayambela broke free down the right of the penalty area, but he was unable to direct his shot on target thanks to good defending from Bradley Carnell.
But in the first minute of injury time Mayambela picked a perfect pass into the danger area that was slid home by Thulasizwe Mbuyane, securing a last-gasp victory for Pirates.