The South Africans edged out Joe Schmidt's men 19-13.
South Africa claimed a 2-1 series win over Ireland after defeating the touring side 19-13 at Port Elizabeth today.
Joe Schmidt's men will be disappointed that they failed to kick-on after their historic first ever win on Springbok soil but will surely take heart from the close margins of defeat in the games.
The home side were perhaps fortunate to finish the game with 15 players following a dangerous tackle in the air from Willie Le Roux, but they can only blame themselves for not showing a clinical edge in attack when the rare opportunities presented themselves.
However, a magnificent defensive effort from Allister Coetzee's well drilled unit, while their wounded pack came out all guns blazing with a dominant scrum that proved pivotal in deciding the fate of the series.
A positive start from Ireland yielded no points early on as Luke Marshall's hands let him down just when the Boks defence was looking stretched.
It handed possession back to the home side and it didn't take them long to push in front as Marshall was caught offside from half centurion Conor Murray's box kick. Elton Jantjies duly punished the indiscipline with a fine kick from range.
Jantjies missed the chance to double the lead soon after as Tendai Mtawarira got the better of Mike Ross in the scrum, a worrying development early on in the game.
The initiative was then handed to Ireland as Willie Le Roux was binned for taking out Tiernan O'Halloran in the air, an incident that saw the Connacht man land straight onto his neck.
The TMO judged it to be only a yellow card offence, stating that the full-back landed on his 'upper back' rather than his head.
With the red card that was shown to CJ Stander in the first test, this didn't look much better than that and its surely going to be a talking point about the consistency of refereeing decisions.
Ireland made the extra numbers count immediately as they barged their way towards the South African line with the likes of Devin Toner, Iain Henderson and Jack McGrath making the hard yards before Luke Marshall got the ball into his hands and crashed over the line.
Jackson converted and Ireland, not for the first time this summer, were in control of the game.
Ireland moved seven ahead when Jackson kicked a penalty from distance, moments after missing an easy kick as Le Roux returned to the field.
The Boks dominance at the scrum continued however, as McGrath was penalised for driving in at an angle on his own scrum, and Jantjies punished the loosehead's indiscipline as he nailed the resulting kick from the tee.
After winning another penalty in the Irish 22', scrum-half Faf de Klerk took it quickly but found the ball to be brilliantly stripped from his clutches by Henderson, giving Ireland the platform to counter.
The ball was shifted through the hands until Marshall cut back in and made an incisive break through South Africa's defence but he was missing the clinical edge this time as his pass to Earls in a two-on-one situation was forward.
The touring side were left to rue their lack of ruthlessness moments later, as an inch perfect Jantjies crossfield chip caught Andrew Trimble out of position which JP Pietersen took advantage of, gathering the ball and crossing the whitewash right on the half-time buzzer.
Jantjies rounded off his impressive first-half performance with an excellent conversion from the touchline, giving the home side a 13-10 lead at the break.
The game resumed at a slower pace after the break with Ireland the first the threaten near the line, as a rolling maul set up in the loose made the yards through the middle in the Boks 22' saw Jackson shift the point of attack, but they were to be denied by a wonderful piece of defensive skill.
The Ulster out-half's looping pass wide to Trimble looked to be the making of a certain try, but De Klerk had to use every inch of his diminutive frame to intercept with one hand and turn possession over.
Tadhg Furlong came in to end Mike Ross' season and renew rivalries with the Beast, but it did little to change the fortunes at the scrum as the dominant South African pack decimated yet another Irish scrum on the halfway mark, which Ruan Combrinck turned into three points with a massive kick.
South Africa's defence was oppressive in the second half as Ireland struggled to gain any change going forward, and the game was beginning to slip away from them when Jantjies kicked his third penalty of the day with just 13 minutes to go.
Joe Schmidt's men were handed a lifeline immediately from the restart though, with Jackson kicking three more points and leaving just six points between the sides entering the final stages.
It meant, for the third week in a row, a tense and nervy finish for both sides as it was just a single score game.
Last week it was the South African bench who had a telling impact on the result, and this week it was up to the Irish bench to swing the momentum back in Ireland's favour.
Eoin Reddan and Sean Cronin both impressed as they upped the intensity in attack for Ireland, but even as they launched one last assault on the Boks line, the South African defence just wouldn't give as de Klerk made an excellent tackle on Keith Earls out wide to isolate the winger and help turn over the ball, just as the buzzer went for full-time.
A 2-1 series defeat is a bitter pill to swallow given the position Ireland found themselves in last week, while they will have grievances about the game today, they were left powerless as they stared into the faces of a resilient Springboks side.