The All Blacks, who have already won the tournament, scored five tries and were good value for the win, with Henry making it third time lucky after two consecutive away losses against the Springboks in as many years in the Tri Nations.
The home side began well but their old problems started to surface with the All Blacks too slick, too fast and too mobile for the Boks, especially in a second half which saw Luke McAlister, Sitiveni Sivivatu, Mils Muliaina and Rico Gear touch down.
Peerless fly-half Dan Carter booted 20 points for the visitors and it needed two late tries from Jaque Fourie to make the scoreline easier on the eye for the hosts.
Percy Montgomery kicked two early penalties to put the Springboks 6-0 up, and even though Carter managed to halve the deficit with a three-pointer for the All Blacks, the hosts stretched the lead through a Fourie du Preez try.
All Blacks captain Richie McCaw, having turned the ball over from Akona Ndungane, then lost possession himself, allowing scrum-half Du Preez to pick up and motor over for the opening try.
Carter brought the All Blacks to within five points with another penalty before Muliaina sped down the near touchline, offloaded to Gear, who cut inside only to be stopped a metre short.
The recycled ball was spread wide and Carter stabbed on for Nemia Tialata, the tighthead prop, to touch down.
Carter stretched the lead to eight points with penalties prior to and after half-time, before the Boks conceded three tries in 14 minutes.
First, McAlister stripped the first line of defence from the halfway line to go over before Jerry Collins took a quick tap and sent Sivivatu past a clutch of forwards to score the third try.
The fourth came when New Zealand forced a turnover, launched a counter attack, and saw Muliaina finish off a flowing move to put his side 38-14 up.
The Boks brought on Ruan Pienaar and Andre Pretorius, and both players made a big difference to the Boks.
Fourie scored the first of his tries when he received a flip pass from Jacques Cronje on a blindside move to power his way over from close range and then got his second 10 minutes later when he was on the shoulder of Jean de Villiers to score under the posts.
That brought the Boks to within 10 points, but as they were edging closer to the All Blacks line, another turnover saw Gear run 70 metres to complete the victory.