Open champion Ernie Els and fellow South African Louis Oosthuizen, the 2010 Open winner, carded 68s to lie joint second.
Paul Lawrie, Thomas Bjorn, Jeev Milkha Singh, Richie Ramsay, Jamie Donaldson, Scott Jamieson and Danny Willett shared fourth spot on 69.
Former paratrooper Thongchai, who is 80th in the world rankings and won last year's Wales Open, made light of the strong winds to post five birdies in an outward 31.
Further birdies at the 10th and 15th holes followed and he cancelled out his only bogey of the day at the 17th with a fine up-and-down from the sand at the 18th for another birdie.
"I made long putts from everywhere. I had 24 or 25 putts today and I haven't putted this well in a long time," Thongchai said.
"It's very, very exciting to come here because I've never been to South Africa before."
The gusting winds and steady rain affected play for much of the afternoon but the 43-year-old remained unaffected and called on the experience he gained from his victory in similar conditions in Wales last year.
"We have no choice, everyone has to play in this and I enjoy it," said the five-times European Tour winner.
"We play most of the time in Europe in conditions like this. I won in the same wind as this in Wales and it was also raining in that one."
Els, who won the 2011 South African Open at the same Durban Country Club course, was also pleased with his seven-birdie effort.
"It was tough. It was the first round of the year and we had to work really hard today. It was blustery right from the first hole but then the rain came really hard for our whole back nine," said the four-times Major champion.
"Just to keep the ball in play and to keep it down - it was a totally different golf course from what I remember yesterday," added the 43-year-old.
Oosthuizen was also lashed by the unseasonal weather but having shown his skill in poor conditions during his commanding Open victory in 2010, the world number six and highest-ranked player in the field had little trouble.
"You couldn't even put up an umbrella because the rain was actually coming in underneath it," he said.
Scot Lawrie, the 1999 Open winner, narrowly missed out on winning a mechanical digger when his tee-shot at the par-three 15th hit the flag and came to rest a couple of inches from the hole.
Twice US Open winner Retief Goosen, returning after five months out following surgery on a "totally disintegrated" back disc, carded a level-par 72 as did Colin Montgomerie.
Triple Major winner Padraig Harrington began his year with a 70.
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