South Africa was forced to draw on all of the experience signified by its record 815 test caps to post its 24th win in 26 test matches against a Welsh team which overcame an early try and a halftime deficit to lead 16-10 with 14 minutes remaining on Sunday.
Tonga-born backrower Toby Faletau scored his first test try to lift Wales to a six-point lead after 53 minutes before Hougaard scored and Morne Steyn added the conversion that clinched South Africa's win.
"What a brilliant start for us, eh?" Springboks coach Peter de Villiers said. "We always knew that this pool is going to be really tough. It was not going to be easy to win in this pool so to be on top of your game in the first match is great."
Fullback James Hook kicked three penalties and a conversion for Wales but debate swirled around a goal he was not awarded. His penalty attempt in the 14th minute, after a high tackle by J.P. Pietersen on Matt Phillips, curled gently from the left of the posts and appeared to pass between the uprights but was flagged away by the linesmen.
Hook's appeal for a review by the television match official was declined and the ruling became an issue of critical importance in a match decided by a single point.
But after the match Welsh players seemed surprised that there was contention around an incident which, for the team, had assumed no great importance. One player after another said the question of Hook's missed penalty had not been raised in the dressing room and none claimed a vantage point that could decide definitevly whether the kick has slipped inside the posts.
All expressed bitter disappointment that a perfect chance for Wales' second win over South Africa in more than 100 years, their first since 1999, had so narrowly eluded them.
"It's soul-destroying," centre Jonathan Davies said. "There's no question we were the better team, we were more physical than they were but a couple of errors cost us the match."
Coach Warren Gatland was equally disappointed that Wales failed, after securing at the world champions' expense surpluses of both possession and territory, to wrest a win from its opening match in Pool D.
"I thought we did everything but win the game," Gatland said. "From that first couple of minutes, I thought we dominated territory and possession and thought we played some great rugby.
"We got ourselves into a chance to win but then we weren't quite good enough."
Even after Hougaard's final try, Wales had two chances to retrieve the match. Hook drifted a penalty attempt wide of the posts nine minutes from fulltime, barely a minute after young flyhalf Rhys Priestland had brushed the posts with an attempted dropped goal.
"The players will just be devastated," Gatland said. "We had a chance (to win): (a) drop goal in front of the posts. Hooky had a chance to kick it. But that's the drama of sport. We'll just take that on the chin; we've got a bonus point out of it. We can take a massive amount of positives out of it in terms of territory and possession.
"I thought that kick in the first half might have been pretty close. Francois Steyn said at halftime in the tunnel that he thought it went over. Those are the things that happen in sport."
South Africa had taken the lead with a try to Frans Steyn after only three minutes, converted from wide out by flyhalf Morne Steyn. Hook cut the lead to 7-3 with his first penalty after nine minutes and it was his second five minutes later which was flagged away by assistant referees George Clancy of Ireland and Vinny Munro of New Zealand.
Hook was successful with his third attempt after 30 minutes, but South Africa took a 10-6 lead to halftime. The Welsh fullback opened the scoring in the second half with his third penalty after nine minutes to cut the Springboks' lead to a point and to raise the spirits of a Welsh team which more than matched the Springboks' physical game.
Led by their captain, the 22-year-old flanker Sam Warburton, Wales began to dominate the Springboks and to unleash some of the enterprise that seemed to set them apart from the more stolid South African team.
A first half of grudging defences had produced 14 missed tackles but no clean linebreaks by either team. Finally, through the middle of the second half, Wales began to find gaps in South Africa's defensive line which was weakened by injuries to centre Jean de Villiers and lock Victor Matfield. De Villiers said the Springboks would take 24 hours to assess the condition of both players but it was likely they would be sidelined for some time.
Tonga-born flanker Toby Faletau crashed through one of the defensive holes in the 53rd minute to score his first test try in his fourth international and Hook converted to give Wales a 16-10 lead. Born at Tofoa in the Pacific Island kingdom of Tonga but now resident at Newport in Welsh rugby's heartland Faletau married the flair of his island heritage with the stoic fortitude of Wales.
He opened the Welsh defence twice more without profit before the Springboks were able to regain some small control of possession. From that foundation and from a sortee into Welsh territory, a penalty, a lineout and a ruck in front of the posts, they fashioned Hougaard's winning try.
"We came so close. We've been quietly confident all week, but just came up short," Warburton said. "We're bitterly disappointed we didn't get the win but shows we're getting closer."
South Africa 17 (Frans Steyn, Francois Hougaard tries; Morne Steyn 2 conversions, penalty), Wales 16 (Toby Faletau try; James Hook conversion, 3 penalties). HT: 10-6.