Declan Kidney's men ran out 15-10 winners over the reigning World Champions thanks to five penalties from Leinster outside-half Jonathan Sexton.
The victory ensured Ireland ended 2009 unbeaten after they won two and drew one of their three autumn internationals.
After claiming their first Six Nations Grand Slam for 61 years, a 20-20 draw with Australia three weeks ago was the only blemish on an otherwise perfect calendar year.
Ireland had to work hard to keep that fabulous record intact, however, as they were forced to overcome a 10-6 half-time deficit against the Springboks.
Schalk Burger's 15th-minute try was the only occasion either side crossed the opposition line but the right boot of Sexton proved more reliable than that of Bok rival Morne Steyn and replacement Ruan Pienaar.
The 24-year-old landed five of his seven attempts at goal, including impressive long-rage efforts in the early stages of either half.
Sexton had the chance to wrap things up with a sixth-successful kick with seven minutes left to play but his uncharacteristic miss made for nervy end to proceedings at Croke Park.
Tendai Mtawaria almost broke Irish hearts with 79 minutes on the clock but the Springbok prop was hauled down less than a metre short as Ireland found themselves outnumbered wide on the right.
South Africa pressed hard with time having gone past the 80 minutes but a huge hit from skipper Brian O'Driscoll on opposite number Jaque Fourie brought about a memorable encounter to a fitting end.
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