Munster fly-half Ronan O'Gara accounted for all the Triple Crown holders'
points - he bagged a try, three penalties and a drop goal - while Percy Montgomery replied with four shots at goal for the tourists.
O'Gara inspired Triple Crown holders Ireland to an 8-3 half-time lead.
He grabbed an opportunist try from a quick tap penalty and then added to the score with a drop-goal which edged out South Africa in a massively entertaining 40 minutes.
A Montgomery penalty gave the Springboks some reward for their first-half efforts as they looked to avoid only a second defeat by Ireland in the history of the fixture.
O'Gara's kicking punished South Africa again just three minutes after the interval with a simple penalty but Montgomery replied in kind shortly after.
The Springboks had emerged from half time as the more composed of the two sides and reaped the rewards by camping in Ireland's 22 and nearly scoring through Montgomery.
But Eddie O'Sullivan's men wrestled back the initiative when a inspirational charge from O'Driscoll swept his side deep into opposition territory and Ireland continued to batter away at South Africa's line.
With the tourists' defence stretched, Burger gave away a penalty for killing the ball which earnt him 10 minutes in the sin-bin and drew three more points from the boot of O'Gara.
O'Gara slotted another three points but South Africa were slowly beginning to tighten the screw and this saw Ireland come under heavy pressure, conceding two penalties which Montgomery kicked.
The Springboks laid siege to the Irish line as the match neared its conclusion, winning a string of penalties as Ireland infringed to keep them out but then spilt the ball forward in the last play of the match to end their hopes of a tour Grand Slam.
Ireland: Girvan Dempsey, Geordan Murphy, Brian O'Driscoll, Shane Horgan, Dennis Hickie, Ronan O'Gara, Peter Stringer, Reggie Corrigan, Shaun Byrne, John Hayes, Malcolm O'Kelly, Paul O'Connell, Simon Easterby, Johnny O'Connor, Anthony Foley.
Replacements: Frank Sheahan, Marcus Horan, Donncha O'Callaghan, Eric Miller, Guy Easterby, David Humphreys, Kevin Maggs.
South Africa: Percy Montgomery, Breyton Paulse, Marius Joubert, De Wet Barry, Ashwin Willemse, Jaco van der Westhuyzen, Fourie Du Preez; Os Du Randt, John Smit, Eddie Andrews; Bakkies Botha, Schalk Burger, Victor Matfield, A J Venter, Joe van Niekerk,
Replacements: Hanyani Shimange, CJ van der Linde, Gerrie Britz, 19 Danie Rossouw, Michael Claassens, Jean de Villiers, Gaffie du Toit or Jaque Fourie.