They responded in fine fashion after the break and again in the first 40 minutes of the second Test before the Boks worked their way back into the game in Pretoria after injuries to Gethin Jenkins and Adam Jones forced uncontested scrums.
"There were massive question marks in the scrum in the first Test in South Africa, which we answered in the second," said Rowntree, who was a specialist scrum coach in 2009 but has now been named forwards coach for 2013.
"We didn't expect the jump to be that much between the provincial games and the first Test last time but the simple fact is that it turned out to be a significant jump.
"It wasn't a case of us being complacent going into the Test series. We played against some good front rows and some big men and we'd done well all tour but then they caught us out.
"The pleasing thing was that we worked it out and fixed it during game time with some changes.
"The second Test was about taking that edge to them and when we went to uncontested scrums it significantly improved their chances because we couldn't tire them out.
"Both Gethin Jenkins and Adam Jones were having a good time in the scrum in the first half of that second Test. When we went to uncontested scrums because of injuries, we lost that advantage."
The Lions pack weren't alone in learning on the job in South Africa, either.
Rowntree himself insists he came back from the Republic a better coach having worked with the likes of Warren Gatland, Sir Ian McGeechan, Rob Howley and Shaun Edwards on what was his third Lions tour but his first as a coach.
"I learnt a lot from some very experienced coaches, some coaching greats in the modern game, with Geech heading up a good crew of coaches," added Rowntree.
"I learnt a lot and that's stood me in good stead in the years that have followed.
"I'm still not the coach I need to be because you are always developing and learning. You never stop."