The Springboks stuttered and were behind on the hour before eventually pulling away to beat the reigning Six Nations champions 37-20 and complete a clean sweep in the two Test series.
The Springboks will play under the new Experimental Law Variations during the annual Tri-Nations series, which begins in July.
And De Villiers revealed that as an on-field preparation for the southern hemisphere competition his side had purposely tried to commit fewer players to the rucks and play more expansively against the Welsh.
"We thought we would try it for the Tri Nations now, because we can't try and change our plans then. By doing it this way, we will favour our play in the Tri Nations," De Villiers said.
His sentiments were echoed by his captain John Smit, who said the breakdown was an important part of why Wales did well in the Test.
"We knew they would be a different kettle of fish this week," he said.
"They had a week to prepare, and were ready for us. We ruled the breakdown last week and this week we had to share the spoils.
"We changed our emphasis at the breakdown, and Wales certainly took their chances. We tried to speed it up, but we should have probably been a little more cautious."
He added: "We started phenomenally but we must learn to be more accurate and be mindful of which periods we need to have a crack and which we shouldn't," he said.
"This is a new team together and we are still trying to adapt to that philosophy on when to crank it up and when to turn it down. That will be the key to how far we will go this year."
Smit had particular praise for Welsh winger Shane Williams, who scored another blistering try as he did in Bloemfontein.
"He is certainly one of those guys we hate to play against him," Smit said.
"To be honest I've never seen someone move as naturally forward and backwards as him and he is one of those guys who makes rugby a special game to watch. I'd rather be watching him on TV than playing against him, but he is a great player."
Springbok attention will now turn to Italy for their one-off Test match at Newlands next weekend before they head into the Tri-Nations against New Zealand and Australia.
De Villiers said he would be discussing the team changes to face Italy on Sunday, but indicated he was likely to experiment with his side in that Test.
"Tomorrow on the plane we will discuss it, not before then," he said.