Both sides scored three tries in a tight match at Loftus Versfeld with home wingers Kurt-Lee Arendse and Cheslin Kolbe crossing for the home side, plus a penalty try awarded by English referee Luke Pearce.
Ireland fullback Jamie Osborne scored on debut with Conor Murray and Ryan Baird adding tries for the touring side in a dramatic final five minutes.
"It's amazing, honestly. I can't explain how great it has been to just come back and be with the boys. This team is so special. What we did in 2023 was for the people so to come back and play here is really special," South Africa captain Siya Kolis said.
The Springboks made many mistakes in a scrappy performance and benefited from marginal refereeing calls as Six Nations champions Ireland stayed in the contest right to the end, despite conceding after three minutes.
South Africa got off to a perfect start, swinging the ball down the line from one side of the pitch to the other before Arendse side stepped inside and burst over for a simple try.
But the Six Nations champions very quickly went on the attack, making it clear the test would be no walkover and forcing furious defence from the hosts.
After an exchange of penalties that put South Africa 13-3 up, Irish fullback Osborne scored in the 35th minute after incredible leg work from winger James Lowe, who kept the ball alive as he was being tackled into touch, to reduce the half-time score to 13-8
After the usually reliable Handre Pollard missed three penalties to stretch South Africa's narrow lead they had a lucky break when Lowe kept a long kick in play only for poacher Kolbe to hack it forward and score.
In a see-saw finish veteran Ireland scrum-half Conor Murray broke through to score, only for South Africa to go down the other end, win a scrum and dramatically drive the Irish back over the line for a penalty try.
Ireland refused to give up, and with South Africa down to 14 men after Arendse was yellow-carded, Baird went over in the corner two minutes from time to reduce the winning margin to seven points.
"There are a lot of positives to take out of our performance but little bits here and there, playing against a side as good as this, they are going to punish you," Ireland captain Peter O'Mahony said.
"We'll go and have a look, fix a few things and look forward to next week."
The sides meet again on Saturday in Durban.Â
