South Africa gave their players four days off to go fishing, visit zoos and explore the east coast of the country following the draw in Brisbane.
Kirsten himself returned home to the rainbow nation to visit his family.
Kirsten said queries over their relaxed build-up to Adelaide were natural.
"It's always something that will come up," he said.
"Sometimes we put in a lot more effort and our preparation for Brisbane we set a very strong foundation. We trained really hard. In fact I commented to the team I think it's the best we've prepared in the time I've been with the team.
"But we also like to create times where we give guys time off. We try and make those decisions because we think they're the right decisions.
"We don't always get it right but we give it our best shot."
Philander woke up on Thursday with a knot in his back and physio staff couldn't relieve the spasms before play started.
Kallis suffered a right hamstring strain for the first time in his career from a seemingly innocuous delivery, but he's been passed fit to bat when South Africa begin their chase.
Kirsten jokingly said the team's two days of hard yakka before Adelaide may have contributed to Philander's injury.
Critics were genuine in questioning whether the changes in intensity between Brisbane and Adelaide had contributed to the breakdowns.
Kirsten said it was impossible to say and argued the world No.1 team had earned some time off and it was no different to what they'd done when they conquered England in the UK earlier this year.
"There's no exact science to it but you can always find a way to criticise in some department," he said.
"I think we've had a long year and we know we had back-to-back Test matches second and third Tests coming up so we didn't feel four days off was too much to give to the players.
"They put in hard yards for us this year.
"We had two really big days of training coming into this Test match and then two top-up days."
- AAP
