And in a second twist, Jamie Roberts has been moved from full-back to inside centre where it is hoped his physical presence will trouble the Springboks.
It is a bold team selection that has drawn a mixed response with critics arguing Gatland has over-reacted to his first defeat as Wales boss.
But the Kiwi stressed that he views the tour to South Africa as a chance to experiment for the future.
"Selection is always a debating point," said Gatland, who was appointed in January.
"It's easy to be negative because if things go wrong you can say you were right, and if things go well it's easy to take the other view.
"We just saw this as an opportunity to make one or two changes.
"James Hook has trained very well at full-back this week while Jamie Roberts has looked good in the midfield.
"Centre is a position Jamie could play long-term and we'll find out more about that tomorrow.
"If we uncover another centre in Jamie then that will be a real positive.
"You could have said playing Jamie at full-back in the first Test last Saturday was a gamble.
"He's been playing winger all season and has had just one game at full-back for Cardiff.
"So on that basis it was also a risk to play him at 15 because he hasn't had much rugby there.
"I understand the criticism but given that we've had a few key players injured this is a chance to experiment and look at other options.
"We needed a player of James' calibre on the field and we felt Stephen Jones looked good at 10, so we were happy to slot him in at full-back instead."
Wales were demolished 43-17 in the opening Test, showing little evidence of the precise rugby that swept them to the Grand Slam title in March.
Reputations are on the line at Loftus Versfeld tomorrow and Gatland has been impressed by the professionalism shown by his squad in their wake of the Bloemfontein debacle.
"Apart from the win the biggest thing we want to get out of the game is a much-improved performance," he said.
"I'm very proud of the way the players have responded to the defeat. We have taken a lot of criticism and know we let ourselves down.
"That was evident on Saturday evening when we went for a meal after the game.
"They made the call that they would not have a drink, instead heading back to the hotel for an early night to prepare themselves for Monday.
"From a coaching point of view that's a very mature response from a group of players that felt they had let themselves and country down.
"A number of individuals were very disappointed with their performances and want to improve on Saturday."