South Africa scored their tries through fullback Damian Willemse, scrumhalf Cobus Reinach, flyhalf Sacha Feinberg-Mngomezulu and a penalty-try, while hooker Dan Sheehan got Ireland’s only score.
Ireland received a 20-minute red card and four yellows, and at one stage had 12 players on the pitch, but some heroic defence and wastefulness from the Springboks kept them in the contest to the end.
The visitors’ victory was built on scrum dominance where they pulverised their hosts, who were perhaps fortunate not to receive more cards at the set-piece.
It is a statement win for the Springboks, though a far from perfect performance as they finish their season in Wales next weekend.
"You can tell by the way I look it was (a crazy game). It's always a tough outing against Ireland, they are a quality side and they kept going until the end," South Africa hooker Malcolm Marx said.
"The character they showed was immense. They had 12 players on the field and still kept us out for a good number of minutes. It shows the bond they have as a team."
South Africa’s first try came inside four minutes as Willemse provided a brilliant finish in the corner.
They burst through several Irish tackles after a collecting a line-out and quick hands sent Willemse into space as he dotted down one-handed with an expert finish.
There was a flashpoint early on when Feinberg-Mngomezulu was perhaps fortunate to get away with a no-arms tackle that resulted in a penalty only and no card, but also a scuffle that involved most players on both sides.
Ireland applied plenty of pressure in the opening quarter and when Sam Prendergast’s penalty came back off the upright, Ireland thought they had got a try via Tadhg Beirne.
But it was disallowed when lock James Ryan flew into a ruck and made head contact with Springbok hooker Malcom Marx and received a 20-minute red card on bunker review, his best possible outcome from a desperately poor piece of play.
It was South Africa’s turn to have a try disallowed when Boan Venter crossed from close range, but Jasper Wiese’s pass to Ruan Nortje in the build-up was forward.
The Springboks were demolishing Ireland at scrum time and that lead to a succession of penalties in the Irish 22.
From another scrum, Canan Moodie carried the ball forward and Ireland wing Tommy O’Brien made head contact in the tackle, and was extremely fortunate to only be penalised and not sent to the sin-bin.
The Springboks took another scrum five metres out and again were dominant, with Ireland infringing repeatedly, and Reinach spotted the gap go over for the visitors’ second score for a 12-0 lead.
One of the Ireland players had to go for their cynical play and it was Sam Prendergast who received the yellow, putting them down to 13 players.
Remarkably, Ireland scored their try while two players down, as they broke through several poor tackles before Sheehan was able to go over for the score.
Ireland were down to 12 players when Jack Crowley was sent to the sin-bin for cynical play at the ruck as he knocked the ball out of the hand of Reinach, and prop Andrew Porter walked for repeated infringements at the scrum.
Not surprisingly, from the next set-piece, Ireland infringed again and referee Matthew Carley had no option but to award the penalty try and the Springboks led 19-7 at halftime.
Ireland scored the first points of the second half despite their numerical disadvantage as Sam Prendergast knocked over a penalty, but it was a brief reprieve.
When the Springboks had another scrum, they pushed Ireland back and ran the ball, with Feinberg-Mngomezulu fending off Jamison Gibson-Park and cutting through the Ireland backline to score.
South Africa were not clinical enough on several entries into the Ireland 22 that kept the home side in the game, and the latter were next to score through a Sam Prendergast penalty.
Sam’s older brother Cian Prendergast was a menace for the Springboks at the breakdown and snuffled several attacks.
Ireland received a fifth card in the game when the visitors put them under more pressure at scrum time and prop Paddy McCarthy was sent to the sin-bin.
The Springboks could not capitalise again thanks to some brilliant Irish defence and work at the breakdown, but did enough to claim the victory despite a late yellow for Grant Williams.
"Chaotic for sure," Ireland captain Caelan Doris said. "I thought we showed some very good character but obviously we're here to show more than that."