Following an opening stand of 126 between Warner (66) and Chris Rogers (107), Australia lost all 10 second-innings wickets for 90 to lose the Port Elizabeth clash by 231 runs as no other batsman made more than six.
Dale Steyn produced a hostile spell of reverse swing to take four for 55 and was well supported by Vernon Philander with two for 39.
Warner admitted both teams had looked to make the ball reverse by throwing it in on the bounce across the outlying wickets.
But he felt South Africa, and De Villiers in particular, went further.
"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 to bring up with the umpires."
Australia's own pacemen struggled to fire as South Africa, led by Hashim Amla's century, declared on 270 for five in their second innings to set a target of 448.
Ryan Harris's 13 wicketless overs went for 74 runs while Peter Siddle - who, like Mitchell Johnson, took two wickets - was also expensive as the ball proved largely unresponsive.
Warner said: "I think it comes down to the umpires warning both teams not to throw the ball into the wicket, which you generally try to do.
"(South Africa) did it better than we did, or more obviously than we did. At the end of the day it comes down to who can do that the best and work on the ball.
"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).
"This time it just didn't work for us because the outfield was probably a little bit moist and (on) day one it was obviously quite hard to get it to reverse as well. Sometimes that happens. "
Either Siddle or Harris could be vulnerable to James Pattinson as coach Darren Lehmann names his team for the decider, while all-rounder Shane Watson is also back in contention after bowling off a full run-up in the nets.
Lehmann said of his attack: "We'll have a look at it, velocity's a big thing for us.
"You certainly need pace, we've seen that with Johnson, Harris and Siddle when he's up and running. We'll have a look at that over the next few days. We'll see how they pull up."
On Watson, he added: "As long as he's bowling overs and he's fit, we would love to have that extra bowler.
"If we have to fit Shane Watson in and someone misses out, it will be really unlucky. It depends on whether we need the fifth bowler and we'll have to wait until we see the wicket. And he's got to be fully fit."
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