Despite their possession and territory, Ireland were unable to break down the stubborn Springbok defence and two second-half penalties was enough to give South Africa a 2-1 series win.
"It's been a great series, a really tough series - exactly what we thought it would be. They're a top side," said Ireland captain Rory Best.
"We came here to win a series, we've fallen short now twice, but six points shows how tight the games have been.
"Our boys have fought valiantly. Unfortunately in the last two Tests the Springboks have been a bit more clinical.
"A lot of people wrote us off before we came here but there are some really young players coming through. There are a lot of boys to come in. The future of Irish rugby is really bright.
"We still think we're good enough to win series like that and eventually we'll take a look back to find out why we didn't."
Scotland did managed a series victory though as the boot of Greig Laidlaw helped them battle from behind to snatch a hard-fought 21-16 win over Japan in Tokyo.
The Scots beat the same opponents 26-13 last week, and had won all five previous contests between the sides, but trailed for much of this game despite Glasgow Warrior Henry Pyrgos' three penalties.
But on 50 minutes, Laidlaw came onto the pitch and landed four penalties in total to give the Scots back-to-back wins.
The day began with Wales coming up against an imperious New Zealand side who saw off the valiant visitors 46-6 in Dunedin to complete a 3-0 series victory.
It means the wait for Wales first win over New Zealand since 1953 continues.
Wing Ben Smith and centre George Moala both crossed in the first half, followed by Beauden Barrett
Fly-half Barrett had a second after half-time and went on to score 26 points in all as Dane Coles and Israel Dagg also crossed.
Ospreys' fly-half Dan Biggar managed the only points for Wales from two penalties.
Follow the Guinness PRO12 on Facebook, join the conversation on Twitter, sign up to our YouTube channel for extensive match highlights and sign up for our newsletter for regular updates on the Guinness PRO12.
63x46.png){kind=logo}