Never before had Italy tasted victory against the Springboks, New Zealand or Australia but capitalized on a succession of South African errors to grind out a narrow win.
Ranked 13th in the world, Italy has been revitalized under new coach Conor O'Shea, who has made the step up to international level after working with English clubs London Irish and Harlequins.
"For us, this is just a start but it's a very good one," the 46-year-old former Ireland international said after Saturday's match.
Captain Sergio Parisse said he was "extremely proud" of his team, before calling the win the most important in the country's history.
"It's the darkest moment of my coaching career. Definitely the toughest," said Allister Coetzee, whose team has dropped from fourth to fifth in the world rankings.
"No disrespect to Italy, but it's not good enough for the Springboks to lose to Italy. I can only congratulate them on an outstanding victory.
"Compared to us, they played without any pressure on them while we looked like a team that lacked self-belief and had a fear of failure."
An early try from Bryan Habana looked to have set the tone for a convincing win, but an error from the restart allowed Italy's South Africa-born Andries Van Schalkwyk to hit back immediately with a try of his own.
Despite enduring a 68-10 thrashing at the hands of New Zealand last week, Italy's players never let their heads drop, even when Damian de Allende got South Africa's second try.
Giovanbattista Venditti ran in for the hosts to level the scores, before a Carlo Canna penalty put Italy narrowly ahead against the two-time World Cup winner.
The margin of victory could have been greater but the referee disallowed a late Italian try, much to the disappointment of the 22,000-strong partisan crowd.
"We are at an all-time low," said former Boks captain Jean de Villiers, who retired from internationals after fracturing his jaw during last year's World Cup -- where South Africa suffered a shock defeat to Japan.
"A lot needs to change for us to go forward. Everyone needs to take responsibility for this, and if they do that, then we have a chance to get it back on track again."
All Blacks' revenge
Meanwhile, world champion New Zealand gained revenge for the shock defeat to Ireland
with a 21-9 win.
Malakai Fekitoa was the hero, crossing to score two tries in a match littered with ill-discipline -- as was their clash in Chicago two weeks ago.
The center was one of two All Blacks to be shown yellow cards, while the injury count reached four inside the first half-hour.
"I'm really proud of the effort the boys put in," Ireland's New Zealand-born coach Joe Schmidt said. "The hub at 10 and 12 (Johnny Sexton and Robbie Henshaw) run your game, and I just felt we lost our shape a bit when they went off.
"At the same time, we put them under immense pressure. But it's frustrating when you pour so much into a game and don't get the result. At 14-9, I thought we were in with a chance."
Elsewhere, an understrength England side ran in nine tries in a 58-15 mauling of Fiji at Twickenham to stay second in the rankings.
Third-ranked Australia beat France 25-23 in Paris, where the home side missed a late drop goal that would have won the match.
Wales, meanwhile, edged past a spirited Japan side 33-30 in Cardiff, requiring a last-minute Sam Davies drop goal to secure victory.