Dale Steyn (4-55) and Vernon Philander (2-39) skittled the Australian line-up to lead South Africa to a series-levelling 231-run win in the second Test in Port Elizabeth.
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But the hosts' tactics have raised eyebrows among the Australians, with Warner singling out wicket-keeper AB de Villiers.
"We were actually questioning whether or not AB de Villiers would get the ball in his hand and with his glove wipe the rough side every ball," Warner told Sky Sports Radio.
"That's another thing we have to try and bring up with the umpires."
Both teams looked to throw the ball into the wicket during the second Test but Warner said South Africa executed the tactic better than Australia.
"I think it comes down to the umpires warning both teams not to throw the ball into the wicket, which you generally try and do," he said.
"They did it better than what we did, or more obvious than what we did. At the end of the day it comes down to who can do that the best and work on the ball."
While South Africa's batsmen enjoyed a good outing, Australia's pace attack struggled as Mitchell Johnson was unable to have the same impact he did in the first Test.
Warner said his team simply failed to do enough work on the ball to get the reverse swing they needed.
"We worked on the ball a lot in England and we got the ball to reverse a lot there, and we got the ball reversing a little at home (against England)," he said.
"This time it just didn't work for us because the outfield was probably a little bit moist under the ground and (on) day one it was obviously quite hard to get it to go reverse as well.
"That's what happens in the game. You have to try and work out how to do that. Sometimes that happens."