Nerurkar finished just 63 seconds behind the winner having been with the leading group until suffering stomach problems midway through the race.
It was a brave performance from the 32-year old former Marlborough College languages teacher, who finished fourth in the 1994 European Championships and seventh in last year's World Championships.
But if Nerurkar thought he had problems with the conditions en route, they were nothing compared to the obstacles Thugwane had overcome preparing for a race which he eventually won by the smallest margin of victory in Olympic marathon history.
After punching the air in delight as he crossed the line in 2hr 12min 36sec - three seconds ahead of Korea's Bong-Ju Lee, and eight seconds clear of the Kenyan bronze medallist, Eric Wainaina - Thugwane described how he had made a remarkable recovery after being shot in a car hijacking in March.
Thugwane, a 5ft 2in security guard at a mineworkers' hostel, still bears the scar of a gunshot wound on his chin from the incident in his home town of Bethel.
"Three or four men got in my car and made me drive away," he said. "They told me to hand over the keys but I refused and there was a bit of a scuffle. They produced a gun and there was shooting. I jumped out of the car while it was still moving and that's how it ended."
Fortunately for Thugwane, the bullet which hit him did little more than graze his chin. More serious was the back injury he suffered when he jumped from the car and he needed medical treatment for several weeks before regaining fitness.
The South African, who won the Honolulu marathon last year and the Cape Town marathon to become South African champion in March - just before the shooting incident - went to the United States to train at altitude near Albuquerque.
"Training there helped me a lot," he said. "At home I train on Table Mountain. My training was very good and I knew if someone broke away I would be able to stay with them. Atlanta is hot but so is my own country."
His triumph came just five days after Hezekiel Sepeng had become the first black South African to win an Olympic medal, taking silver in the 800 metres.
"I am so happy for all runners and my country," Thugwane said. "This is a victory for them all."
Although weather conditions were cooler than predicted, the pack stayed bunched and fairly slow until Thugwane pushed out on his own after 30 kilometres. He was soon followed by Lee and Wainaina and the three opened up a big gap on the rest.
The South African, the first runner from his continent to win the marathon since Mamo Wolde of Ethiopia in 1968, had the most in reserve as the three men surged into the stadium together. The finish was significantly closer than the narrowest previously seen in the Olympics, when Johannes Kolehmainene of Finland won in Antwerp, 1920, with 12.8sec to spare.
Nerurkar was dispirited at the finish. "I hit a bad patch after 25 kilometres," he said. "I just got a stomach problem and could not get it out of my system until about 32km. I was probably about 12th or 13th then but I realised I was running quite well again and started moving through the field, but then the gaps between runners just got bigger and bigger.
"I came here to try and win a medal and I was in great shape so I am disappointed. It was a tough course and the conditions were difficult but they were what I expected."
Nerurkar came home in 2:13:39, just 19 seconds behind Spain's Martin Fiz who took the world title in Sweden. Peter Whitehead, who was fourth in Gothenburg, finished well down in 2:22:37 while Welshman Steve Brace came home 60th in 2:23:28.
Thugwane's was not the only Olympic marathon record of the day. Abdul- Basir Wasiqi, a 21-year-old from Afghanistan, finished in 4:24:17, the slowest recorded time in an Olympic final. Wasiqi, who walked for much of the second half of the course, was originally told he was too slow to finish in the main stadium, where preparations were already underway for staging the closing ceremony later in the evening.
But after a change of heart from the organisers, the turfs which had begun to be laid on the track were removed by volunteers and Wasiqi was allowed to cross the same line Thugwane had passed over two hours earlier, to widespread applause. It was a belated PR success for the host city of these beleaguered Games.Reuse content