Hook's appeal for a review by the television match official was declined and the ruling assumed critical importance in a match decided by a single point.
South Africa had taken an early lead with a try to fullback 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 surprisingly flagged away by assistant referees George Clancy of Ireland and Vinny Munro of New Zealand.
The kick, from about 38 meters to the left of the posts, appeared to curl inside the right-hand upright but the touch judges, who were well sighted quickly ruled it had missed. It would have cut the lead to a single point and might have acted as a spur to a Welsh team rallying bravely after conceding from Steyn's early try.
"I thought that kick in the first half might have been pretty close,'' Wales coach Warran Gatland said. Francois Steyn said at halftime in the tunnel that he thought it went over. Those are the things that happen in sport.''
Gatland said Wales had other chances to seal the match, and his players "will just be devastated.''
"We had a chance: drop goal in front of the posts. Hooky had a chance to kick it. But that's the drama of sport,'' he said. "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.''
Hook was successful with his third attempt at goal, 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 had gained surpluses of territory and possession in the first spell.
Led by their captain, the 22-year-old flanker Sam Warburton, Wales began to physically 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 defenses 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.
Tonga-born flanker Toby Faletau crashed through one of those 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 defense 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.''
Springboks coach Peter de Villiers described the match as "a great test of character'' and captain John Smit commended Wales for fully stretching his team in the 400th test in South Africa's history. Smit marked his own milestone, as captain of South Africa for a record 80th time in his 107th test match.
"Wales played some good rugby, they kept us in their half so we couldn't really get a chance to play ourselves into this game,'' he said. "So when we got a chance, luckily we took it. But I tell you what, close game nice to get through it.
"The nerves for this game were unbelievable. I think it had a lot to do with our build-up, how we left (South Africa), the pressure and what it meant to this pool. The greatest reward was that we came through by a point and will be a most valuable lesson for us, again fighting our way back from a pretty sticky situation.''
South Africa 17 (Francois Steyn, Francois Hougaard tries; Morne Steyn 2 conversions, penalty) def. Wales 16 (Toby Faletau try; James Hook conversion, 3 penalties). HT: 10-6.
- AP