The South Africans did not realise they had won until glancing over at the replay on the big screen, surging to catch up silver medallists Britain, early leaders Denmark in bronze and Australia in fourth.
It marks a historic first Olympic rowing gold for the nation, while Brits Chris Bartley, Rob Williams and the Chambers brothers, Peter and Richard, can take pride in a silver finish after a late charge of their own to catch up to the Danes.
South Africa triumphed in a time of six minutes 02:84, from Team GB a quarter of a second back. Denmark were a further 0.07 of a second behind the British.
Younger brother Peter admitted that while it was fantastic to get the silver medal, he and his crewmates were left thinking about what could have been.
“We are gutted,” said the Northern Ireland-born rower.
“We were unlucky to get a silver with those conditions. We're delighted with silver but we wanted to get gold.
"Fair play to the South Africans – they won that fair and square. They still are Olympic medals and as a team we can't ask for much more."
Williams shared Chambers’ disappointment with the result, but admitted the race was too tight to call.
He said: “We came to win, but it's an incredibly tight event. You can't take anything for granted.
"The crowd are fantastic. That last 200 metres would have been a lot harder if they hadn't been there."
Earlier in the morning, Nathan Cohen and Joseph Sullivan of New Zealand won a tense battle for gold in the men's double sculls final, with Britain finishing in fifth.
The double world champions had been sitting in fifth place for most of the race before they upped their rate and moved through the field in the final 300 metres.
Italy claimed silver while early pace-setters Slovenia settled for bronze.
Britain's Bill Lucas and Sam Townsend struggled to keep the pace of an unpredictable second half of the final and finished out of the medal places.
Concluding the day's medal competition at Eton Dorney was another fifth-placed finish for Britain, as their women's eight were well off the pace of a race won by the United States.
The American boat took a lead of a third of a length by 500 metres over the Canadians and the Netherlands before extending that as they powered down Dorney Lake, holding on to win by about two thirds of a length.
Canada finished in second with the Netherlands in third.
The American women's cox punched the air with delight as her crew fell back into their boat with exhaustion.