Ireland captain Rory Best felt South Africa’s stronger cutting edge proved decisive after his side lost 19-13 in the third Test to suffer a 2-1 series defeat.
Springboks fly-half Elton Jantjies led his team to victory, kicking 11 points to add to JP Pietersen’s try and a penalty from Ruan Combrinck.
Luke Marshall’s touch down and eight points from the boot of Paddy Jackson kept the Irish in contention but they fell just short in Port Elizabeth.
Best told Sky Sports: “It’s been a great series but a really, really tough series. It’s exactly what we thought it would be.
“Nothing was ever given easily, we knew we had to defend really well.
“They’re a top side, we came here to win a series, we’ve fallen short twice.
“Our boys have fought valiantly and we’ve really put everything in. Unfortunately in the last two Tests, the Springboks have just been a little bit more clinical.”
Ireland headed into the final Test level after their 26-20 victory in Cape Town two weeks ago was followed by a 32-26 defeat in Johannesburg last weekend.
Head coach Joe Schmidt expressed some regret at losing the series but was happy to help Ireland record a first-ever victory over South Africa on opposition soil.
“It’s not a lost cause,” he told Sky Sports. “Three six-point results (wining margins); two of them unfortunately didn’t go our way.
“If you’d offered me one win and a couple of other close results like that before the tour, I probably would have taken it because there’s a little bit of history there but at the same time when you get as close as we did, it’s disappointing.”