Henry was frustrated with what he saw as deliberate injury breaks being employed by the Springboks to slow down his side's play.
He said: "I was disappointed with the injuries. The game has been slowed down. It occurred in the Super 14 and some teams go down more than others."
Henry was also unhappy with his side's performance, despite coming from behind to win thanks to Daniel Carter's 25 points from the boot.
He continued: "The players were not happy with the way we played out there and neither should they be. They didn't play as well as they should.
"There were a lot of aspects of our game that we didn't do well.
"Carter is a beautiful player. He had a big game, he didn't miss one of his kicks and you can't ask a lot more than that."
South Africa coach Jake White defended his side's tactics and was delighted with the performance after last week's 49-0 demolition at the hands of Australia.
He said: "It was never going to be pretty and it was always going to be difficult for the boys to play with confidence after what happened last week.
"All Blacks Tests are never easy but I think 35-17 was not a true reflection."